Modulating light response pathways in plants, increasing light-related tolerances in plants, and increasing biomass in plants

ABSTRACT

Methods and materials for modulating low light and/or shade tolerance, and red light specific responses in plants are disclosed. For example, nucleic acids encoding low light and/or SD+EODFR-tolerance polypeptides are disclosed as well as methods for using such nucleic acids to transform plant cells. Also disclosed are plants having increased low light and/or SD+EODFR tolerance. In addition, methods and materials involved in increasing UV-B tolerance in plants and methods and materials involved in modulating biomass levels in plants are provided.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation-in-part application of and claimspriority to (a) U.S. patent application Ser. No. 12/863,102, filed Apr.11, 2011, which is a National Stage application under 35 U.S.C. § 371 ofInternational Application No. PCT/US2009/031292, filed Jan. 16, 2009,which claims the benefit of priority under 35 U.S.C. § 119(e) to U.S.Provisional Patent Application Ser. No. 61/021,943, filed Jan. 18, 2008,(b) U.S. patent application Ser. No. 12/373,134, filed Apr. 6, 2010,which is a National Stage application under 35 U.S.C. § 371 ofInternational Application No. PCT/US2007/073154, filed Jul. 10, 2007,which claims the benefit of priority under 35 U.S.C. § 119(e) to U.S.Provisional Patent Application Ser. No. 60/819,763, filed Jul. 10, 2006,(c) U.S. patent application Ser. No. 12/513,086, filed Apr. 23, 2010,which is a National Stage application under 35 U.S.C. § 371 ofInternational Application No. PCT/US2007/083495, filed Nov. 2, 2007,which claims the benefit of priority under 35 U.S.C. § 119(e) to U.S.Provisional Patent Application Ser. No. 60/856,613, filed Nov. 3, 2006,(d) U.S. patent application Ser. No. 12/515,687, filed Apr. 6, 2010,which is a National Stage application under 35 U.S.C. § 371 ofInternational Application No. PCT/US2007/085237, filed Nov. 20, 2007,which claims the benefit of priority under 35 U.S.C. § 119(e) to U.S.Provisional Patent Application Ser. No. 60/860,145, filed Nov. 20, 2006,(e) U.S. patent application Ser. No. 12/307,561, filed Nov. 23, 2009,which is a National Stage application under 35 U.S.C. § 371 ofInternational Application No. PCT/US2007/072877, filed Jul. 5, 2007,which claims priority under 35 U.S.C. § 119(e) to U.S. ProvisionalPatent Application Ser. No. 60/818,569, filed Jul. 5, 2006, and (f) U.S.patent application Ser. No. 13/119,572, filed Mar. 17, 2011, which is aNational Stage application under 35 U.S.C. § 371 of InternationalApplication No. PCT/US2009/057116, filed Sep. 16, 2009, which claims thebenefit of priority under 35 U.S.C. § 119(e) to U.S. Provisional PatentApplication Ser. No. 61/097,789, filed Sep. 17, 2008. The disclosures ofthese prior applications are considered part of (and are incorporated byreference in their entirety in) the disclosure of this application.

TECHNICAL FIELD

This document relates to methods and materials involved in plant shadeand/or low light tolerance, and red light specific responses. Forexample, this document provides plants having increased shade and/or lowlight tolerance as well as materials and methods for making plantshaving increased shade and/or low light tolerance. This document alsorelates to methods and materials involved in increasing UV-B tolerancein plants and methods and materials involved in modulating biomasslevels in plants.

BACKGROUND

Light is the source of energy that fuels plant growth throughphotosynthesis. Light is also a developmental signal that modulatesmorphogenesis, such as de-etiolation and the transition to reproductivedevelopment. Since plants cannot choose their surroundings, they areforced to adapt their growth to ambient light conditions and haveevolved complex mechanisms for monitoring the quantity and quality ofthe surrounding light. For example, many kinds of plants respond togrowth under dense canopies or at high densities by growing faster andtaller (Cerdan and Chory (2003) Nature, 423:881). Densely planted cropstend to place energy into stem and petiole elongation to lift the leavesinto the sunlight rather than putting energy into storage orreproductive structures. The response to low light conditions and/orshade conditions negatively affects crop yields by reducing the amountof harvestable products such as seeds, fruits and tubers. In addition,tall spindly plants tend to be less wind resistant and lodge moreeasily, further reducing crop yield.

There is a continuing need for plants that can thrive under less thanoptimal environmental conditions. One strategy to improve a plant'sability to withstand suboptimal environmental conditions relies upontraditional plant breeding methods. Another approach involves geneticmanipulation of plant characteristics through the introduction ofexogenous nucleic acids conferring a desirable trait.

SUMMARY

The spectral energy distribution of daylight is dramatically altered byvegetation. Light reflected from neighboring vegetation is depleted inred (R) wavelengths, but remains rich in far-red (FR) wavelengths. It isdesirable to have plants that exhibit increased shade tolerance. Plantshaving increased shade tolerance described herein exhibit an increasedtolerance to shade conditions, in particular. Short Day plus End-of-DayFar-Red (SD+EODFR) conditions. Wild-type plants typically exhibit shadeavoidance responses to SD+EODFR conditions, whereas theSD+EODFR-tolerant plants described herein display a reduction in thelevel of shade avoidance responses relative to the level of shadeavoidance responses displayed by non-SD+EODFR-tolerant plants.

The quantity of light can dictate the eventual biomass and yield ofplants. Wild-type plants typically exhibit low light responses, whereasthe low light-tolerant plants described herein display a reduction inthe level of low light responses relative to the level of low lightresponses displayed by non-low light-tolerant plants.

Increasing the SD+EODFR and/or low light tolerance of plants canincrease the crop yields of such plants, which can benefit both foodconsumers and producers. This document provides methods and materialsrelated to plants having increased shade and/or low light tolerance. Forexample, this document provides transgenic plants having increasedSD+EODFR and/or low light tolerance, nucleic acids used to generatetransgenic plants having increased SD+EODFR and/or low light tolerance,and methods for making plants having increased SD+EODFR and/or low lighttolerance. Such plants may be useful to produce biomass which may beconverted to a liquid fuel or other chemicals and/or to produce cropswith increased yield and/or quality.

Methods of producing a plant are provided herein. In one aspect, amethod comprises growing a plant cell comprising an exogenous nucleicacid. The exogenous nucleic acid comprises a regulatory region operablylinked to a nucleotide sequence encoding a polypeptide. The HiddenMarkov Model (HMM) bit score of the amino acid sequence of thepolypeptide is greater than about 20, using an HMM generated from theamino acid sequences depicted in one of FIGS. 1-24. A plant producedfrom the cell has a difference in low light or SD+EODFR tolerance ascompared to a control plant that does not comprise the exogenous nucleicacid.

In another aspect, the exogenous nucleic acid comprises a regulatoryregion operably linked to a nucleotide sequence encoding a polypeptidehaving 80 percent or greater sequence identity to an amino acid sequenceset forth in SEQ ID NOs:3, 5, 7, 9, 10, 12, 14, 16, 18, 20, 22, 24, 25,26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 49, 51, 53, 55, 57, 59,60, 61, 62, 63, 65, 67, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 89, 90,91, 93, 95, 96, 97, 98, 99, 100, 101, 102, 103, 105, 107, 109, 111, 113,115, 116, 117, 118, 119, 120, 121, 122, 124, 126, 129, 130, 131, 132,133, 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159,161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183, 185, 187,188, 189, 191, 193, 195, 197, 199, 201, 203, 205, 207, 209, 211, 213,215, 217, 219, 221, 223, 225, 227, 229, 230, 231, 232, 233, 234, 235,236, 237, 238, 239, 241, 243, 245, 247, 249, 251, 253, 255, 257, 259,261, 262, 264, 266, 268, 270, 271, 273, 275, 277, 279, 281, 283, 285,287, 289, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302,303, 304, 306, 308, 310, 312, 314, 317, 319, 321, 323, 325, 327, 329,330, 331, 332, 334, 337, 339, 341, 343, 344, 346, 347, 348, 349, 350,351, 352, 353, 354, 355, 357, 359, 361, 362, 364, 365, 366, 367, 368,370, 372, 374, 376, 378, 379, 381, 383, 385, 387, 389, 391, 393, 395,397, 399, 401, 403, 405, 407, 409, 411, 413, 415, 417, 419, 421, 423,425, 427, 429, 431, 433, 435, 437, 439, 441, 443, 445, 447, 449, 451,453, 456, 457, 458, 459, 460, 462, 464, 466, 468, 470, 472, 474, 475,477, 478, 479, 480, 481, 482, 483, 484, 485, 486, 487, 488, 489, 491,493, 494, 495, 496, 497, 498, 499, 501, 503, 505, 507, 508, 509, 510,511, 512, 514, 515, 516, 518, 520, 521, 522, 523, 524, 525, 526, 527,528, 529, 530, 531, 532, 533, 534, 535, 536, 538, 539, 541, 542, 543,544, 545, 546, 547, 548, 549, 550, 552, 554, 555, 556, 557, 558, 559,560, 561, 562, 563, 564, 565, 567, 570, 572, 574, 576, 578, 579, 580,582, 584, 586, 588, 590, 592, 594, 596, 598, 600, 601, 603, 606, 607,608, 609, 611, 613, 615, 616, 617, 618, 620, 621, 622, 624, 625, 626,628, 629, 631, 634, 636, 637, 638, 639, 641, 644, 645, 647, 649, 651,653, 655, 657, 659, 661, 663, 665, 667, 669, 671, 673, 675, 676, 678,680, 682, 684, 686, 688, 690, 692, 694, 695, 697, 699, 701, 702, 704,706, 708, 709, 711, 712, 713, 714, 716, 718, 720, 721, 723, 725, 726,728, 730, 732, 734, 736, 738, 740, 741, 742, 743, 744, 745, 747, 749,750, 751, 753, 755, 757, 759, 761, 762, 763, 764, 765, 767, 769, 771,773, 774, 776, 778, 779, 780, 782, 783, 784, 786, 788, 790, 792, 794,795, 796, 797, 798, 799, 800, 801, 802, 803, 804, 805, 806, 807, 808,809, 810, 811, 812, 813, 814, 815, 816, 817, 818, 819, 820, 821, 822,823, 824, 826, 827, 829, 830, 831, 832, 833, 834, 835, 837, 838, 839,840, 841, 843, 845, 847, 850, 851, 853, 855, 857, 859, 861, 862, 863,864, 865, 866, 868, 870, 872, 874, 876, 877, 879, 881, 883, 885, 887,889, 891, 893, 895, 897, 898, 900, 902, 904, 907, 909, 911, 913, 915,917, 919, 920, 922, 923, 924, 926, 928, 929, 930, 931, 932, 934, 936,937, 938, 939, 940, 941, 943, 945, 947, 948, 949, 950, 953, 955, 957,959, 961, 963, 965, 966, 967, 969, 971, 973, 975, 977, 979, 981, 983,985, 987, 989, 991, 993, 995, 997, 999, 1001, 1003, 1005, 1007, 1009,1011, 1013, 1014, 1015, 1016, 1018, 1024, 1025, 1027, 1029, 1030, 1032,1033, 1035, 1037, 1039, 1040, 1042, 1043, 1044, 1047, 1049, 1051, 1053,1055, 1057, 1059, 1061, 1063, 1065, 1067, 1068, 1069, 1071, 1072, 1073,1074, 1075, 1077, 1078, 1080, 1081, 1083, 1085, 1087, 1089, 1091, 1093,1095, 1097, 1098, 1099, 1100, 1101, 1103, 1105, 1107, 1109, 1111, 1113,1115, 1117, 1119, 1121, 1123, 1125, 1127, 1129, 1131, 1133, 1134, 1135,1136, 1137, 1138, 1139, 1141, 1143, 1145, 1147, 1149, 1151, 1153, 1155,1157, 1159, 1160, 1161, 1162, 1164, 1166, 1168, 1170, 1172, 1174, 1176,1178, 1180, 1182, 1184, 1186, 1188, 1190, 1192, 1194, 1196, 1198, 1199,1200, 1201, 1202, 1203, 1204, 1206, 1208, 1209, 1211, 1213, 1214, 1215,1216, 1217, 1219, 1221, 1223, 1225, 1227, 1229, 1230, 1232, 1234, 1236,1238, 1240, 1242, 1244, 1246, 1248, 1250, 1252, 1254, 1255, 1256, 1257,1258, 1259, 1260, 1261, 1262, 1263, 1264, 1266, 1268, 1270, 1272, 1274,1277, 1279, 1281, 1283, 1285, 1287, 1289, 1291, 1293, 1294, 1295, 1297,1298, 1299, 1301, 1303, 1305, 1307, 1309, 1311, 1313, 1315, 1317, 1319,1321, 1322, 1323, 1324, 1325, 1326, 1327, 1328, 1329, 1330, 1331, 1332,1334, 1336, 1338, 1340, 1342, 1344, 1347, 1349, 1351, 1352, 1353, 1355,1357, 1358, 1360, 1362, 1364, 1366, 1367, 1368, 1370, 1372, 1374, 1375,1377, 1379, 1381, 1383, 1385, 1387, 1389, 1391, 1393, 1395, 1397, 1399,1401, 1402, 1404, 1406, 1408, 1410, 1411, 1412, 1413, 1414, 1415, 1417,1419, 1421, 1422, 1423, 1424, 1425, 1426, 1427, 1429, 1430, 1431, 1433,1434, 1435, 1436, 1438, 1439, 1440, 1442, 1444, 1446, 1448, 1450, 1452,1457, 1458, 1460, 1462, 1464, 1466, 1467, 1468, 1469, 1471, 1473, 1475,1477, 1478, 1479, 1480, 1481, 1482, 1483, 1484, 1485, 1486, 1488, 1490,1492, 1494, 1497, 1499, 1501, 1502, 1503, 1504, 1505, 1506, 1508, 1510,1511, 1512, 1513, 1514, 1515, 1516, 1518, 1519, 1520, 1521, 1522, 1523,1524, 1525, 1527, 1528, 1529, 1531, 1532, 1533, 1534, 1535, 1536, 1540,1541, 1543, 1545, 1547, 1549, 1551, 1553, 1554, 1555, 1556, 1557, 1558,1559, 1561, 1563, 1564, 1565, 1566, 1567, 1568, 1570, 1572, 1574, 1576,1578, 1580, 1582, 1584, 1587, 1589, 1591, 1593, 1594, 1596, 1597, 1598,1599, 1600, 1601, 1602, 1603, 1604, 1605, 1606, 1607, 1609, 1611, 1612,1613, 1614, 1615, 1616, 1617, 1618, 1619, 1620, 1621, 1623, 1625, 1630,1631, 1632, 1635, 1637, 1639, 1641, 1642, 1643, 1644, 1646, 1648, 1650,1651, 1652, 1653, 1654, 1655, 1657, 1659, 1661, 1663, 1665, 1667, 1669,1671, 1673, 1675, 1677, 1679, 1681, 1682, 1684, 1686, 1688, 1690, 1692,1694, 1696, 1698, 1699, 1700, 1701, 1702, 1703, 1704, 1705, 1707, 1709,1711, 1713, 1715, 1717, 1719, 1720, 1721, 1722, 1723, 1725, 1727, 1729,1730, 1732, 1734, 1736, 1738, 1739, 1740, 1741, 1742, 1743, 1744, 1745,1746, 1748, 1750, 1751, 1752, 1754, 1756, 1758, 1760, 1762, 1764, 1766,1767, 1768, 1769, 1770, 1771, 1772, 1773, 1774, 1775, 1776, 1777, 1778,1780, 1782, 1784, 1786, 1788, 1790, 1792, 1794, 1796, 1798, 1800, 1802,1804, 1805, 1806, 1807, 1808, 1809, 1810, 1811, 1812, 1813, 1814, 1815,1816, 1817, 1818, 1819, 1820, 1821, 1822, 1823, 1824, 1825, 1826, 1827,1828, 1829, 1830, 1831, 1832, 1833, 1834, 1835, 1836, 1837, 1838, 1839,1840, 1842, 1843, 1844, 1845, 1846, 1847, 1848, 1850, 1852, 1854, 1856,1858, 1859, 1860, 1861, 1862, 1863, 1864, 1865, 1866, 1867, 1869, 1870,1871, 1873, 1875, 1877, 1879, 1881, 1883, 1885, 1887, 1889, 1891, 1893,1895, 1897, 1899, 1901, 1903, 1905, 1907, 1909, 1911, 1913, 1915, 1917,1919, 1921, 1923, 1925, 1927, 1929, 1931, 1933, 1935, 1937, 1939, 1941,1943, 1945, 1947, 1949, 1951, 1953, 1955, 1957, 1959, 1961, 1963, 1965,1967, 1969, 1971, 1973, 1975, 1977, 1979, 1981, 1983, 1985, 1987, 1989,1991, 1993, 1995, 1997, 1999, 2001, 2003, 2005, 2007, 2009, 2011, 2013,2015, 2017, 2019, 2021, 2023, 2025, 2027, 2029, 2030, 2031, 2032, 2033,2034, 2035, 2036, 2037, 2038, 2039, 2040, 2041, 2042, 2043, 2044, 2045,2046, 2047, 2048, 2049, 2050, 2051, 2052, 2053, 2054, 2055, 2056, 2057,2058, 2059, 2060, 2061, 2062, 2063, 2064, 2065, 2066, 2067, 2069, 2070,2072, 2074, 2076, 2078, 2080, 2081, 2083, 2084, 2085, 2087, 2089, 2091,2093, 2095, 2097, 2099, 2101, 2103, 2105, 2107, 2109, 2111, 2113, 2114,2115, 2116, 2117, 2118, 2119, 2120, 2121, 2123, 2125, 2127, 2129, 2131,2133, 2135, 2136, 2137, 2138, 2139, 2140, 2141, 2142, 2143, 2144, 2146,2148, 2150, 2152, 2154, 2156, 2158, 2160, 2162, 2164, 2166, 2168, 2170,2172, 2174, 2176, 2178, 2180, 2182, 2183, 2184, 2185, 2186, 2187, 2188,2189, 2190, 2191, 2192, 2193, 2194, 2195, 2196, 2197, 2198, 2199, 2200,2201, 2202, 2203, 2204, 2205, 2206, 2207, 2208, 2209, 2210, 2211, 2212,2213, 2214, 2215, 2216, 2217, 2218, 2219, 2220, 2221, 2222, 2223, 2224,2225, 2226, 2227, 2228, 2229, 2230, 2231, 2232, 2233, 2234, 2235, 2236,2237, 2238, 2239, 2240, 2241, 2242, 2243, 2244, 2245, 2246, 2247, 2248,2249, 2250, 2251, 2252, 2253, 2254, 2255, 2256, 2257, 2258, 2259, 2260,2261, 2262, 2263, 2264, 2266, 2268, 2269, 2270, 2271, 2272, 2273, 2274,2275, 2276, 2277, 2278, 2280, 2282, 2284, 2286, 2288, 2290, 2292, 2294,2296, 2298, 2300, 2302, 2304, 2306, 2308, 2310, 2312, 2314, 2316, 2318,2320, 2322, 2323, 2324, 2325, 2326, 2327, 2328, 2329, 2330, 2331, 2332,2333, 2334, 2335, 2336, 2337, 2338, 2339, 2340, 2341, 2342, 2343, 2344,2345, 2346, 2347, 2348, 2350, 2352, 2354, 2356, 2358, 2360, 2362, 2364,2366, 2368, 2370, 2372, 2374, 2375, 2376, 2377, 2378, 2379, 2380, or2381. A plant produced from the plant cell has a difference in low lightor SD+EODFR tolerance as compared to a control plant that does notcomprise the exogenous nucleic acid.

In one aspect, the polypeptide further comprises a CDI domain having 70percent or greater sequence identity to the CDI domain of SEQ ID NO:70.In another aspect, the polypeptide further comprises an AUX/IAA domainhaving 70 percent or greater sequence identity to the AUX/IAA domain ofSEQ ID NO:129 or SEQ ID NO:1347. In another aspect, the polypeptidefurther comprises a homeobox domain having 70 percent or greatersequence identity to the homeobox domain of SEQ ID NO:317. In anotheraspect, the polypeptide further comprises a zf_C3HC4 domain having 70percent or greater sequence identity to the zf_C3HC4 domain of SEQ IDNO:337. In another aspect, the polypeptide further comprises a B-boxzinc finger domain having 70 percent or greater sequence identity to theB-box zinc finger domain of SEQ ID NO:456 and a CCT motif having 70percent or greater sequence identity to the CCT motif of SEQ ID NO:456.In another aspect, the polypeptide further comprises a FAD_binding_7domain having 70 percent or greater sequence identity to theFAD_binding_7 domain of SEQ ID NO:538 or SEQ ID NO:1497 and a DNAphotolyase domain having 70 percent or greater sequence identity to theDNA photolyase domain of SEQ ID NO:538 or SEQ ID NO:1497. In anotheraspect, the polypeptide further comprises a zf_Dof domain having 70percent or greater sequence identity to the zf_Dof domain of SEQ IDNO:606. In another aspect, the polypeptide further comprises an AP2domain having 70 percent or greater sequence identity to the AP2 domainof SEQ ID NO:645. In another aspect, the polypeptide further comprises aVQ motif having 70 percent or greater sequence identity to the VQ motifof SEQ ID NO:850. In another aspect, the polypeptide further comprises azf_C2H2 domain having 70 percent or greater sequence identity to thezf_C2H2 domain of SEQ ID NO:907. In another aspect, the polypeptidefurther comprises a TCP domain having 70 percent or greater sequenceidentity to the TCP domain of SEQ ID NO:1151. In another aspect, thepolypeptide further comprises an F-box domain having 70 percent orgreater sequence identity to the F-box domain of SEQ ID NO:1277. Inanother aspect, the polypeptide further comprises a zf_CCCH domainhaving 70 percent or greater sequence identity to the zf_CCCH domain ofSEQ ID NO:1457. In another aspect, the polypeptide further comprises aPOX domain having 70 percent or greater sequence identity to the POXdomain of SEQ ID NO:1540 and a homeobox domain having 70 percent orgreater sequence identity to the homeobox domain of SEQ ID NO:1540. Inanother aspect, the polypeptide further comprises an HSF-typeDNA-binding domain having 70 percent or greater sequence identity to theHSF-type DNA-binding domain of SEQ ID NO:1587. In another aspect, thepolypeptide further comprises a SAM_1 domain having 70 percent orgreater sequence identity to the SAM_1 domain of SEQ ID NO:1635 and aDRMBL domain having 70 percent or greater sequence identity to the DRMBLdomain of SEQ ID NO:1635.

In another aspect, a method of producing a plant comprises growing aplant cell comprising an exogenous nucleic acid, where the exogenousnucleic acid comprises a regulatory region operably linked to anucleotide sequence having 80 percent or greater sequence identity to anucleotide sequence, or a fragment thereof, set forth in SEQ ID NOs:1,2, 4, 6, 8, 11, 13, 15, 17, 19, 21, 23, 27, 29, 31, 33, 35, 37, 39, 41,43, 45, 47, 50, 52, 54, 56, 58, 64, 66, 68, 69, 71, 73, 75, 77, 79, 81,83, 85, 87, 92, 94, 104, 106, 108, 110, 112, 114, 123, 125, 127, 128,134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160,162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 190,192, 194, 196, 198, 200, 202, 204, 206, 208, 210, 212, 214, 216, 218,220, 222, 224, 226, 228, 240, 242, 244, 246, 248, 250, 252, 254, 256,258, 260, 263, 265, 267, 269, 272, 274, 276, 278, 280, 282, 284, 286,288, 290, 305, 307, 309, 311, 313, 315, 316, 318, 320, 322, 324, 326,328, 333, 335, 336, 338, 340, 342, 345, 356, 358, 360, 363, 369, 371,373, 375, 377, 380, 382, 384, 386, 388, 390, 392, 394, 396, 398, 400,402, 404, 406, 408, 410, 412, 414, 416, 418, 420, 422, 424, 426, 428,430, 432, 434, 436, 438, 440, 442, 444, 446, 448, 450, 452, 454, 455,461, 463, 465, 467, 469, 471, 473, 476, 490, 492, 500, 502, 504, 506,513, 517, 519, 537, 540, 551, 553, 566, 568, 569, 571, 573, 575, 577,581, 583, 585, 587, 589, 591, 593, 595, 597, 599, 602, 604, 605, 610,612, 614, 619, 623, 627, 630, 632, 633, 635, 640, 642, 643, 646, 648,650, 652, 654, 656, 658, 660, 662, 664, 666, 668, 670, 672, 674, 677,679, 681, 683, 685, 687, 689, 691, 693, 696, 698, 700, 703, 705, 707,710, 715, 717, 719, 722, 724, 727, 729, 731, 733, 735, 737, 739, 746,748, 752, 754, 756, 758, 760, 766, 768, 770, 772, 775, 777, 781, 785,787, 789, 791, 793, 825, 828, 836, 842, 844, 846, 848, 849, 852, 854,856, 858, 860, 867, 869, 871, 873, 875, 878, 880, 882, 884, 886, 888,890, 892, 894, 896, 899, 901, 903, 905, 906, 908, 910, 912, 914, 916,918, 921, 925, 927, 933, 935, 942, 944, 946, 951, 952, 954, 956, 958,960, 962, 964, 968, 970, 972, 974, 976, 978, 980, 982, 984, 986, 988,990, 992, 994, 996, 998, 1000, 1002, 1004, 1006, 1008, 1010, 1012, 1017,1019, 1020, 1021, 1022, 1023, 1026, 1028, 1031, 1034, 1036, 1038, 1041,1045, 1046, 1048, 1050, 1052, 1054, 1056, 1058, 1060, 1062, 1064, 1066,1070, 1076, 1079, 1082, 1084, 1086, 1088, 1090, 1092, 1094, 1096, 1102,1104, 1106, 1108, 1110, 1112, 1114, 1116, 1118, 1120, 1122, 1124, 1126,1128, 1130, 1132, 1140, 1142, 1144, 1146, 1148, 1150, 1152, 1154, 1156,1158, 1163, 1165, 1167, 1169, 1171, 1173, 1175, 1177, 1179, 1181, 1183,1185, 1187, 1189, 1191, 1193, 1195, 1197, 1205, 1207, 1210, 1212, 1218,1220, 1222, 1224, 1226, 1228, 1231, 1233, 1235, 1237, 1239, 1241, 1243,1245, 1247, 1249, 1251, 1253, 1265, 1267, 1269, 1271, 1273, 1275, 1276,1278, 1280, 1282, 1284, 1286, 1288, 1290, 1292, 1296, 1300, 1302, 1304,1306, 1308, 1310, 1312, 1314, 1316, 1318, 1320, 1333, 1335, 1337, 1339,1341, 1343, 1345, 1346, 1348, 1350, 1354, 1356, 1359, 1361, 1363, 1365,1369, 1371, 1373, 1376, 1378, 1380, 1382, 1384, 1386, 1388, 1390, 1392,1394, 1396, 1398, 1400, 1403, 1405, 1407, 1409, 1416, 1418, 1420, 1428,1432, 1437, 1441, 1443, 1445, 1447, 1449, 1451, 1453, 1454, 1455, 1456,1459, 1461, 1463, 1465, 1470, 1472, 1474, 1476, 1487, 1489, 1491, 1493,1495, 1496, 1498, 1500, 1507, 1509, 1517, 1526, 1530, 1537, 1538, 1539,1542, 1544, 1546, 1548, 1550, 1552, 1560, 1562, 1569, 1571, 1573, 1575,1577, 1579, 1581, 1583, 1585, 1586, 1588, 1590, 1592, 1595, 1608, 1610,1622, 1624, 1626, 1627, 1628, 1629, 1633, 1634, 1636, 1638, 1640, 1645,1647, 1649, 1656, 1658, 1660, 1662, 1664, 1666, 1668, 1670, 1672, 1674,1676, 1678, 1680, 1683, 1685, 1687, 1689, 1691, 1693, 1695, 1697, 1706,1708, 1710, 1712, 1714, 1716, 1718, 1724, 1726, 1728, 1731, 1733, 1735,1737, 1747, 1749, 1753, 1755, 1757, 1759, 1761, 1763, 1765, 1779, 1781,1783, 1785, 1787, 1789, 1791, 1793, 1795, 1797, 1799, 1801, 1803, 1841,1849, 1851, 1853, 1855, 1857, 1868, 1872, 1874, 1876, 1878, 1880, 1882,1884, 1886, 1888, 1890, 1892, 1894, 1896, 1898, 1900, 1902, 1904, 1906,1908, 1910, 1912, 1914, 1916, 1918, 1920, 1922, 1924, 1926, 1928, 1930,1932, 1934, 1936, 1938, 1940, 1942, 1944, 1946, 1948, 1950, 1952, 1954,1956, 1958, 1960, 1962, 1964, 1966, 1968, 1970, 1972, 1974, 1976, 1978,1980, 1982, 1984, 1986, 1988, 1990, 1992, 1994, 1996, 1998, 2000, 2002,2004, 2006, 2008, 2010, 2012, 2014, 2016, 2018, 2020, 2022, 2024, 2026,2028, 2068, 2071, 2073, 2075, 2077, 2079, 2082, 2086, 2088, 2090, 2092,2094, 2096, 2098, 2100, 2102, 2104, 2106, 2108, 2110, 2112, 2122, 2124,2126, 2128, 2130, 2132, 2134, 2145, 2147, 2149, 2151, 2153, 2155, 2157,2159, 2161, 2163, 2165, 2167, 2169, 2171, 2173, 2175, 2177, 2179, 2181,2265, 2267, 2279, 2281, 2283, 2285, 2287, 2289, 2291, 2293, 2295, 2297,2299, 2301, 2303, 2305, 2307, 2309, 2311, 2313, 2315, 2317, 2319, 2321,2349, 2351, 2353, 2355, 2357, 2359, 2361, 2363, 2365, 2367, 2369, 2371,or 2373. A plant produced from the plant cell has a difference in lowlight or SD+EODFR tolerance as compared to a control plant that does notcomprise the exogenous nucleic acid.

Methods of modulating low light tolerance in a plant are providedherein. In one aspect, a method comprises introducing into a plant cellan exogenous nucleic acid, that comprises a regulatory region operablylinked to a nucleotide sequence encoding a polypeptide. The HMM bitscore of the amino acid sequence of the polypeptide is greater thanabout 20, using an HMM generated from the amino acid sequences depictedin one of FIGS. 1-24. A plant produced from the plant cell has adifference in low light tolerance as compared to a control plant thatdoes not comprise the exogenous nucleic acid.

In another aspect, a method comprises introducing into a plant cell anexogenous nucleic acid that comprises a regulatory region operablylinked to a nucleotide sequence encoding a polypeptide having 80 percentor greater sequence identity to an amino acid sequence set forth in SEQID NOs:3, 5, 7, 9, 10, 12, 14, 16, 18, 20, 22, 24, 25, 26, 28, 30, 32,34, 36, 38, 40, 42, 44, 46, 48, 49, 51, 53, 55, 57, 59, 60, 61, 62, 63,65, 67, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 89, 90, 91, 93, 95, 96,97, 98, 99, 100, 101, 102, 103, 105, 107, 109, 111, 113, 115, 116, 117,118, 119, 120, 121, 122, 124, 126, 129, 130, 131, 132, 133, 135, 137,139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165,167, 169, 171, 173, 175, 177, 179, 181, 183, 185, 187, 188, 189, 191,193, 195, 197, 199, 201, 203, 205, 207, 209, 211, 213, 215, 217, 219,221, 223, 225, 227, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238,239, 241, 243, 245, 247, 249, 251, 253, 255, 257, 259, 261, 262, 264,266, 268, 270, 271, 273, 275, 277, 279, 281, 283, 285, 287, 289, 291,292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 306,308, 310, 312, 314, 317, 319, 321, 323, 325, 327, 329, 330, 331, 332,334, 337, 339, 341, 343, 344, 346, 347, 348, 349, 350, 351, 352, 353,354, 355, 357, 359, 361, 362, 364, 365, 366, 367, 368, 370, 372, 374,376, 378, 379, 381, 383, 385, 387, 389, 391, 393, 395, 397, 399, 401,403, 405, 407, 409, 411, 413, 415, 417, 419, 421, 423, 425, 427, 429,431, 433, 435, 437, 439, 441, 443, 445, 447, 449, 451, 453, 456, 457,458, 459, 460, 462, 464, 466, 468, 470, 472, 474, 475, 477, 478, 479,480, 481, 482, 483, 484, 485, 486, 487, 488, 489, 491, 493, 494, 495,496, 497, 498, 499, 501, 503, 505, 507, 508, 509, 510, 511, 512, 514,515, 516, 518, 520, 521, 522, 523, 524, 525, 526, 527, 528, 529, 530,531, 532, 533, 534, 535, 536, 538, 539, 541, 542, 543, 544, 545, 546,547, 548, 549, 550, 552, 554, 555, 556, 557, 558, 559, 560, 561, 562,563, 564, 565, 567, 570, 572, 574, 576, 578, 579, 580, 582, 584, 586,588, 590, 592, 594, 596, 598, 600, 601, 603, 606, 607, 608, 609, 611,613, 615, 616, 617, 618, 620, 621, 622, 624, 625, 626, 628, 629, 631,634, 636, 637, 638, 639, 641, 644, 645, 647, 649, 651, 653, 655, 657,659, 661, 663, 665, 667, 669, 671, 673, 675, 676, 678, 680, 682, 684,686, 688, 690, 692, 694, 695, 697, 699, 701, 702, 704, 706, 708, 709,711, 712, 713, 714, 716, 718, 720, 721, 723, 725, 726, 728, 730, 732,734, 736, 738, 740, 741, 742, 743, 744, 745, 747, 749, 750, 751, 753,755, 757, 759, 761, 762, 763, 764, 765, 767, 769, 771, 773, 774, 776,778, 779, 780, 782, 783, 784, 786, 788, 790, 792, 794, 795, 796, 797,798, 799, 800, 801, 802, 803, 804, 805, 806, 807, 808, 809, 810, 811,812, 813, 814, 815, 816, 817, 818, 819, 820, 821, 822, 823, 824, 826,827, 829, 830, 831, 832, 833, 834, 835, 837, 838, 839, 840, 841, 843,845, 847, 850, 851, 853, 855, 857, 859, 861, 862, 863, 864, 865, 866,868, 870, 872, 874, 876, 877, 879, 881, 883, 885, 887, 889, 891, 893,895, 897, 898, 900, 902, 904, 907, 909, 911, 913, 915, 917, 919, 920,922, 923, 924, 926, 928, 929, 930, 931, 932, 934, 936, 937, 938, 939,940, 941, 943, 945, 947, 948, 949, 950, 953, 955, 957, 959, 961, 963,965, 966, 967, 969, 971, 973, 975, 977, 979, 981, 983, 985, 987, 989,991, 993, 995, 997, 999, 1001, 1003, 1005, 1007, 1009, 1011, 1013, 1014,1015, 1016, 1018, 1024, 1025, 1027, 1029, 1030, 1032, 1033, 1035, 1037,1039, 1040, 1042, 1043, 1044, 1047, 1049, 1051, 1053, 1055, 1057, 1059,1061, 1063, 1065, 1067, 1068, 1069, 1071, 1072, 1073, 1074, 1075, 1077,1078, 1080, 1081, 1083, 1085, 1087, 1089, 1091, 1093, 1095, 1097, 1098,1099, 1100, 1101, 1103, 1105, 1107, 1109, 1111, 1113, 1115, 1117, 1119,1121, 1123, 1125, 1127, 1129, 1131, 1133, 1134, 1135, 1136, 1137, 1138,1139, 1141, 1143, 1145, 1147, 1149, 1151, 1153, 1155, 1157, 1159, 1160,1161, 1162, 1164, 1166, 1168, 1170, 1172, 1174, 1176, 1178, 1180, 1182,1184, 1186, 1188, 1190, 1192, 1194, 1196, 1198, 1199, 1200, 1201, 1202,1203, 1204, 1206, 1208, 1209, 1211, 1213, 1214, 1215, 1216, 1217, 1219,1221, 1223, 1225, 1227, 1229, 1230, 1232, 1234, 1236, 1238, 1240, 1242,1244, 1246, 1248, 1250, 1252, 1254, 1255, 1256, 1257, 1258, 1259, 1260,1261, 1262, 1263, 1264, 1266, 1268, 1270, 1272, 1274, 1277, 1279, 1281,1283, 1285, 1287, 1289, 1291, 1293, 1294, 1295, 1297, 1298, 1299, 1301,1303, 1305, 1307, 1309, 1311, 1313, 1315, 1317, 1319, 1321, 1322, 1323,1324, 1325, 1326, 1327, 1328, 1329, 1330, 1331, 1332, 1334, 1336, 1338,1340, 1342, 1344, 1347, 1349, 1351, 1352, 1353, 1355, 1357, 1358, 1360,1362, 1364, 1366, 1367, 1368, 1370, 1372, 1374, 1375, 1377, 1379, 1381,1383, 1385, 1387, 1389, 1391, 1393, 1395, 1397, 1399, 1401, 1402, 1404,1406, 1408, 1410, 1411, 1412, 1413, 1414, 1415, 1417, 1419, 1421, 1422,1423, 1424, 1425, 1426, 1427, 1429, 1430, 1431, 1433, 1434, 1435, 1436,1438, 1439, 1440, 1442, 1444, 1446, 1448, 1450, 1452, 1457, 1458, 1460,1462, 1464, 1466, 1467, 1468, 1469, 1471, 1473, 1475, 1477, 1478, 1479,1480, 1481, 1482, 1483, 1484, 1485, 1486, 1488, 1490, 1492, 1494, 1497,1499, 1501, 1502, 1503, 1504, 1505, 1506, 1508, 1510, 1511, 1512, 1513,1514, 1515, 1516, 1518, 1519, 1520, 1521, 1522, 1523, 1524, 1525, 1527,1528, 1529, 1531, 1532, 1533, 1534, 1535, 1536, 1540, 1541, 1543, 1545,1547, 1549, 1551, 1553, 1554, 1555, 1556, 1557, 1558, 1559, 1561, 1563,1564, 1565, 1566, 1567, 1568, 1570, 1572, 1574, 1576, 1578, 1580, 1582,1584, 1587, 1589, 1591, 1593, 1594, 1596, 1597, 1598, 1599, 1600, 1601,1602, 1603, 1604, 1605, 1606, 1607, 1609, 1611, 1612, 1613, 1614, 1615,1616, 1617, 1618, 1619, 1620, 1621, 1623, 1625, 1630, 1631, 1632, 1635,1637, 1639, 1641, 1642, 1643, 1644, 1646, 1648, 1650, 1651, 1652, 1653,1654, 1655, 1657, 1659, 1661, 1663, 1665, 1667, 1669, 1671, 1673, 1675,1677, 1679, 1681, 1682, 1684, 1686, 1688, 1690, 1692, 1694, 1696, 1698,1699, 1700, 1701, 1702, 1703, 1704, 1705, 1707, 1709, 1711, 1713, 1715,1717, 1719, 1720, 1721, 1722, 1723, 1725, 1727, 1729, 1730, 1732, 1734,1736, 1738, 1739, 1740, 1741, 1742, 1743, 1744, 1745, 1746, 1748, 1750,1751, 1752, 1754, 1756, 1758, 1760, 1762, 1764, 1766, 1767, 1768, 1769,1770, 1771, 1772, 1773, 1774, 1775, 1776, 1777, 1778, 1780, 1782, 1784,1786, 1788, 1790, 1792, 1794, 1796, 1798, 1800, 1802, 1804, 1805, 1806,1807, 1808, 1809, 1810, 1811, 1812, 1813, 1814, 1815, 1816, 1817, 1818,1819, 1820, 1821, 1822, 1823, 1824, 1825, 1826, 1827, 1828, 1829, 1830,1831, 1832, 1833, 1834, 1835, 1836, 1837, 1838, 1839, 1840, 1842, 1843,1844, 1845, 1846, 1847, 1848, 1850, 1852, 1854, 1856, 1858, 1859, 1860,1861, 1862, 1863, 1864, 1865, 1866, 1867, 1869, 1870, 1871, 1873, 1875,1877, 1879, 1881, 1883, 1885, 1887, 1889, 1891, 1893, 1895, 1897, 1899,1901, 1903, 1905, 1907, 1909, 1911, 1913, 1915, 1917, 1919, 1921, 1923,1925, 1927, 1929, 1931, 1933, 1935, 1937, 1939, 1941, 1943, 1945, 1947,1949, 1951, 1953, 1955, 1957, 1959, 1961, 1963, 1965, 1967, 1969, 1971,1973, 1975, 1977, 1979, 1981, 1983, 1985, 1987, 1989, 1991, 1993, 1995,1997, 1999, 2001, 2003, 2005, 2007, 2009, 2011, 2013, 2015, 2017, 2019,2021, 2023, 2025, 2027, 2029, 2030, 2031, 2032, 2033, 2034, 2035, 2036,2037, 2038, 2039, 2040, 2041, 2042, 2043, 2044, 2045, 2046, 2047, 2048,2049, 2050, 2051, 2052, 2053, 2054, 2055, 2056, 2057, 2058, 2059, 2060,2061, 2062, 2063, 2064, 2065, 2066, 2067, 2069, 2070, 2072, 2074, 2076,2078, 2080, 2081, 2083, 2084, 2085, 2087, 2089, 2091, 2093, 2095, 2097,2099, 2101, 2103, 2105, 2107, 2109, 2111, 2113, 2114, 2115, 2116, 2117,2118, 2119, 2120, 2121, 2123, 2125, 2127, 2129, 2131, 2133, 2135, 2136,2137, 2138, 2139, 2140, 2141, 2142, 2143, 2144, 2146, 2148, 2150, 2152,2154, 2156, 2158, 2160, 2162, 2164, 2166, 2168, 2170, 2172, 2174, 2176,2178, 2180, 2182, 2183, 2184, 2185, 2186, 2187, 2188, 2189, 2190, 2191,2192, 2193, 2194, 2195, 2196, 2197, 2198, 2199, 2200, 2201, 2202, 2203,2204, 2205, 2206, 2207, 2208, 2209, 2210, 2211, 2212, 2213, 2214, 2215,2216, 2217, 2218, 2219, 2220, 2221, 2222, 2223, 2224, 2225, 2226, 2227,2228, 2229, 2230, 2231, 2232, 2233, 2234, 2235, 2236, 2237, 2238, 2239,2240, 2241, 2242, 2243, 2244, 2245, 2246, 2247, 2248, 2249, 2250, 2251,2252, 2253, 2254, 2255, 2256, 2257, 2258, 2259, 2260, 2261, 2262, 2263,2264, 2266, 2268, 2269, 2270, 2271, 2272, 2273, 2274, 2275, 2276, 2277,2278, 2280, 2282, 2284, 2286, 2288, 2290, 2292, 2294, 2296, 2298, 2300,2302, 2304, 2306, 2308, 2310, 2312, 2314, 2316, 2318, 2320, 2322, 2323,2324, 2325, 2326, 2327, 2328, 2329, 2330, 2331, 2332, 2333, 2334, 2335,2336, 2337, 2338, 2339, 2340, 2341, 2342, 2343, 2344, 2345, 2346, 2347,2348, 2350, 2352, 2354, 2356, 2358, 2360, 2362, 2364, 2366, 2368, 2370,2372, 2374, 2375, 2376, 2377, 2378, 2379, 2380, or 2381. A plantproduced from the plant cell has a difference in low light tolerance ascompared to a control plant that does not comprise the exogenous nucleicacid.

In another aspect, a method comprises introducing into a plant cell anexogenous nucleic acid, that comprises a regulatory region operablylinked to a nucleotide sequence having 80 percent or greater sequenceidentity to a nucleotide sequence set forth in SEQ ID NOs:1, 2, 4, 6, 8,11, 13, 15, 17, 19, 21, 23, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47,50, 52, 54, 56, 58, 64, 66, 68, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87,92, 94, 104, 106, 108, 110, 112, 114, 123, 125, 127, 128, 134, 136, 138,140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166,168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 190, 192, 194, 196,198, 200, 202, 204, 206, 208, 210, 212, 214, 216, 218, 220, 222, 224,226, 228, 240, 242, 244, 246, 248, 250, 252, 254, 256, 258, 260, 263,265, 267, 269, 272, 274, 276, 278, 280, 282, 284, 286, 288, 290, 305,307, 309, 311, 313, 315, 316, 318, 320, 322, 324, 326, 328, 333, 335,336, 338, 340, 342, 345, 356, 358, 360, 363, 369, 371, 373, 375, 377,380, 382, 384, 386, 388, 390, 392, 394, 396, 398, 400, 402, 404, 406,408, 410, 412, 414, 416, 418, 420, 422, 424, 426, 428, 430, 432, 434,436, 438, 440, 442, 444, 446, 448, 450, 452, 454, 455, 461, 463, 465,467, 469, 471, 473, 476, 490, 492, 500, 502, 504, 506, 513, 517, 519,537, 540, 551, 553, 566, 568, 569, 571, 573, 575, 577, 581, 583, 585,587, 589, 591, 593, 595, 597, 599, 602, 604, 605, 610, 612, 614, 619,623, 627, 630, 632, 633, 635, 640, 642, 643, 646, 648, 650, 652, 654,656, 658, 660, 662, 664, 666, 668, 670, 672, 674, 677, 679, 681, 683,685, 687, 689, 691, 693, 696, 698, 700, 703, 705, 707, 710, 715, 717,719, 722, 724, 727, 729, 731, 733, 735, 737, 739, 746, 748, 752, 754,756, 758, 760, 766, 768, 770, 772, 775, 777, 781, 785, 787, 789, 791,793, 825, 828, 836, 842, 844, 846, 848, 849, 852, 854, 856, 858, 860,867, 869, 871, 873, 875, 878, 880, 882, 884, 886, 888, 890, 892, 894,896, 899, 901, 903, 905, 906, 908, 910, 912, 914, 916, 918, 921, 925,927, 933, 935, 942, 944, 946, 951, 952, 954, 956, 958, 960, 962, 964,968, 970, 972, 974, 976, 978, 980, 982, 984, 986, 988, 990, 992, 994,996, 998, 1000, 1002, 1004, 1006, 1008, 1010, 1012, 1017, 1019, 1020,1021, 1022, 1023, 1026, 1028, 1031, 1034, 1036, 1038, 1041, 1045, 1046,1048, 1050, 1052, 1054, 1056, 1058, 1060, 1062, 1064, 1066, 1070, 1076,1079, 1082, 1084, 1086, 1088, 1090, 1092, 1094, 1096, 1102, 1104, 1106,1108, 1110, 1112, 1114, 1116, 1118, 1120, 1122, 1124, 1126, 1128, 1130,1132, 1140, 1142, 1144, 1146, 1148, 1150, 1152, 1154, 1156, 1158, 1163,1165, 1167, 1169, 1171, 1173, 1175, 1177, 1179, 1181, 1183, 1185, 1187,1189, 1191, 1193, 1195, 1197, 1205, 1207, 1210, 1212, 1218, 1220, 1222,1224, 1226, 1228, 1231, 1233, 1235, 1237, 1239, 1241, 1243, 1245, 1247,1249, 1251, 1253, 1265, 1267, 1269, 1271, 1273, 1275, 1276, 1278, 1280,1282, 1284, 1286, 1288, 1290, 1292, 1296, 1300, 1302, 1304, 1306, 1308,1310, 1312, 1314, 1316, 1318, 1320, 1333, 1335, 1337, 1339, 1341, 1343,1345, 1346, 1348, 1350, 1354, 1356, 1359, 1361, 1363, 1365, 1369, 1371,1373, 1376, 1378, 1380, 1382, 1384, 1386, 1388, 1390, 1392, 1394, 1396,1398, 1400, 1403, 1405, 1407, 1409, 1416, 1418, 1420, 1428, 1432, 1437,1441, 1443, 1445, 1447, 1449, 1451, 1453, 1454, 1455, 1456, 1459, 1461,1463, 1465, 1470, 1472, 1474, 1476, 1487, 1489, 1491, 1493, 1495, 1496,1498, 1500, 1507, 1509, 1517, 1526, 1530, 1537, 1538, 1539, 1542, 1544,1546, 1548, 1550, 1552, 1560, 1562, 1569, 1571, 1573, 1575, 1577, 1579,1581, 1583, 1585, 1586, 1588, 1590, 1592, 1595, 1608, 1610, 1622, 1624,1626, 1627, 1628, 1629, 1633, 1634, 1636, 1638, 1640, 1645, 1647, 1649,1656, 1658, 1660, 1662, 1664, 1666, 1668, 1670, 1672, 1674, 1676, 1678,1680, 1683, 1685, 1687, 1689, 1691, 1693, 1695, 1697, 1706, 1708, 1710,1712, 1714, 1716, 1718, 1724, 1726, 1728, 1731, 1733, 1735, 1737, 1747,1749, 1753, 1755, 1757, 1759, 1761, 1763, 1765, 1779, 1781, 1783, 1785,1787, 1789, 1791, 1793, 1795, 1797, 1799, 1801, 1803, 1841, 1849, 1851,1853, 1855, 1857, 1868, 1872, 1874, 1876, 1878, 1880, 1882, 1884, 1886,1888, 1890, 1892, 1894, 1896, 1898, 1900, 1902, 1904, 1906, 1908, 1910,1912, 1914, 1916, 1918, 1920, 1922, 1924, 1926, 1928, 1930, 1932, 1934,1936, 1938, 1940, 1942, 1944, 1946, 1948, 1950, 1952, 1954, 1956, 1958,1960, 1962, 1964, 1966, 1968, 1970, 1972, 1974, 1976, 1978, 1980, 1982,1984, 1986, 1988, 1990, 1992, 1994, 1996, 1998, 2000, 2002, 2004, 2006,2008, 2010, 2012, 2014, 2016, 2018, 2020, 2022, 2024, 2026, 2028, 2068,2071, 2073, 2075, 2077, 2079, 2082, 2086, 2088, 2090, 2092, 2094, 2096,2098, 2100, 2102, 2104, 2106, 2108, 2110, 2112, 2122, 2124, 2126, 2128,2130, 2132, 2134, 2145, 2147, 2149, 2151, 2153, 2155, 2157, 2159, 2161,2163, 2165, 2167, 2169, 2171, 2173, 2175, 2177, 2179, 2181, 2265, 2267,2279, 2281, 2283, 2285, 2287, 2289, 2291, 2293, 2295, 2297, 2299, 2301,2303, 2305, 2307, 2309, 2311, 2313, 2315, 2317, 2319, 2321, 2349, 2351,2353, 2355, 2357, 2359, 2361, 2363, 2365, 2367, 2369, 2371, or 2373, ora fragment thereof. A plant produced from the plant cell has adifference in low light tolerance as compared to a control plant thatdoes not comprise the exogenous nucleic acid.

Methods of modulating SD+EODFR tolerance in a plant are provided herein.In one aspect, a method comprises introducing into a plant cell anexogenous nucleic acid, that comprises a regulatory region operablylinked to a nucleotide sequence encoding a polypeptide. The HMM bitscore of the amino acid sequence of the polypeptide is greater thanabout 20, using an HMM generated from the amino acid sequences depictedin one of FIG. 16 or 24-27. A plant produced from the plant cell has adifference in SD+EODFR tolerance as compared to a control plant thatdoes not comprise the exogenous nucleic acid.

In another aspect, a method comprises introducing into a plant cell anexogenous nucleic acid that comprises a regulatory region operablylinked to a nucleotide sequence encoding a polypeptide having 80 percentor greater sequence identity to an amino acid sequence set forth in SEQID NOs:538, 539, 541, 542, 543, 544, 545, 546, 547, 548, 549, 550, 552,554, 555, 556, 557, 558, 559, 560, 561, 562, 563, 564, 565, 567, 570,572, 574, 576, 578, 579, 580, 582, 584, 586, 588, 590, 592, 594, 596,598, 600, 601, 603, 606, 607, 608, 609, 611, 613, 615, 616, 617, 618,620, 621, 622, 624, 625, 626, 628, 629, 631, 1347, 1349, 1351, 1352,1353, 1355, 1357, 1358, 1360, 1362, 1364, 1366, 1367, 1368, 1370, 1372,1374, 1375, 1377, 1379, 1381, 1383, 1385, 1387, 1389, 1391, 1393, 1395,1397, 1399, 1401, 1402, 1404, 1406, 1408, 1410, 1411, 1412, 1413, 1414,1415, 1417, 1419, 1421, 1422, 1423, 1424, 1425, 1426, 1427, 1429, 1430,1431, 1433, 1434, 1435, 1436, 1438, 1439, 1440, 1442, 1444, 1446, 1448,1450, 1452, 1540, 1541, 1543, 1545, 1547, 1549, 1551, 1553, 1554, 1555,1556, 1557, 1558, 1559, 1561, 1563, 1564, 1565, 1566, 1567, 1568, 1570,1572, 1574, 1576, 1578, 1580, 1582, 1584, 1679, 1681, 1682, 1748, 1750,1751, 1752, 1850, 1852, 1854, 1856, 1858, 1859, 1860, 1861, 1862, 1863,1864, 1865, 1866, 1867, 1869, 1870, 1871, 1873, 1875, 1877, 1879, 1881,1883, 1885, 1887, 1889, 1891, 1893, 1895, 1897, 1899, 1901, 1903, 1905,1907, 2268, 2269, 2270, 2271, 2272, 2273, 2274, 2275, 2276, 2277, or2278. A plant produced from the plant cell has a difference in SD+EODFRtolerance as compared to a control plant that does not comprise theexogenous nucleic acid.

In another aspect, a method comprises introducing into a plant cell anexogenous nucleic acid, that comprises a regulatory region operablylinked to a nucleotide sequence having 80 percent or greater sequenceidentity to a nucleotide sequence set forth in SEQ ID NOs:537, 540, 551,553, 566, 568, 569, 571, 573, 575, 577, 581, 583, 585, 587, 589, 591,593, 595, 597, 599, 602, 604, 605, 610, 612, 614, 619, 623, 627, 630,1345, 1346, 1348, 1350, 1354, 1356, 1359, 1361, 1363, 1365, 1369, 1371,1373, 1376, 1378, 1380, 1382, 1384, 1386, 1388, 1390, 1392, 1394, 1396,1398, 1400, 1403, 1405, 1407, 1409, 1416, 1418, 1420, 1428, 1432, 1437,1441, 1443, 1445, 1447, 1449, 1451, 1537, 1538, 1539, 1542, 1544, 1546,1548, 1550, 1552, 1560, 1562, 1569, 1571, 1573, 1575, 1577, 1579, 1581,1583, 1678, 1680, 1747, 1749, 1849, 1851, 1853, 1855, 1857, 1868, 1872,1874, 1876, 1878, 1880, 1882, 1884, 1886, 1888, 1890, 1892, 1894, 1896,1898, 1900, 1902, 1904, 1906, and 2267, or a fragment thereof. A plantproduced from the plant cell has a difference in SD+EODFR tolerance ascompared to a control plant that does not comprise the exogenous nucleicacid.

Plant cells comprising an exogenous nucleic acid are provided herein. Inone aspect, the exogenous nucleic acid comprises a regulatory regionoperably linked to a nucleotide sequence encoding a polypeptide. The HMMbit score of the amino acid sequence of the polypeptide is greater thanabout 20, using an HMM based on the amino acid sequences depicted in oneof FIGS. 1-24. A plant produced from the cells has a difference in lowlight or SD+EODFR tolerance as compared to a control plant that does notcomprise the exogenous nucleic acid. In another aspect, the exogenousnucleic acid comprises a regulatory region operably linked to anucleotide sequence encoding a polypeptide having 80 percent or greatersequence identity to an amino acid sequence selected from the groupconsisting of SEQ ID NOs:3, 5, 7, 9, 10, 12, 14, 16, 18, 20, 22, 24, 25,26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 49, 51, 53, 55, 57, 59,60, 61, 62, 63, 65, 67, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 89, 90,91, 93, 95, 96, 97, 98, 99, 100, 101, 102, 103, 105, 107, 109, 111, 113,115, 116, 117, 118, 119, 120, 121, 122, 124, 126, 129, 130, 131, 132,133, 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159,161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183, 185, 187,188, 189, 191, 193, 195, 197, 199, 201, 203, 205, 207, 209, 211, 213,215, 217, 219, 221, 223, 225, 227, 229, 230, 231, 232, 233, 234, 235,236, 237, 238, 239, 241, 243, 245, 247, 249, 251, 253, 255, 257, 259,261, 262, 264, 266, 268, 270, 271, 273, 275, 277, 279, 281, 283, 285,287, 289, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302,303, 304, 306, 308, 310, 312, 314, 317, 319, 321, 323, 325, 327, 329,330, 331, 332, 334, 337, 339, 341, 343, 344, 346, 347, 348, 349, 350,351, 352, 353, 354, 355, 357, 359, 361, 362, 364, 365, 366, 367, 368,370, 372, 374, 376, 378, 379, 381, 383, 385, 387, 389, 391, 393, 395,397, 399, 401, 403, 405, 407, 409, 411, 413, 415, 417, 419, 421, 423,425, 427, 429, 431, 433, 435, 437, 439, 441, 443, 445, 447, 449, 451,453, 456, 457, 458, 459, 460, 462, 464, 466, 468, 470, 472, 474, 475,477, 478, 479, 480, 481, 482, 483, 484, 485, 486, 487, 488, 489, 491,493, 494, 495, 496, 497, 498, 499, 501, 503, 505, 507, 508, 509, 510,511, 512, 514, 515, 516, 518, 520, 521, 522, 523, 524, 525, 526, 527,528, 529, 530, 531, 532, 533, 534, 535, 536, 538, 539, 541, 542, 543,544, 545, 546, 547, 548, 549, 550, 552, 554, 555, 556, 557, 558, 559,560, 561, 562, 563, 564, 565, 567, 570, 572, 574, 576, 578, 579, 580,582, 584, 586, 588, 590, 592, 594, 596, 598, 600, 601, 603, 606, 607,608, 609, 611, 613, 615, 616, 617, 618, 620, 621, 622, 624, 625, 626,628, 629, 631, 634, 636, 637, 638, 639, 641, 644, 645, 647, 649, 651,653, 655, 657, 659, 661, 663, 665, 667, 669, 671, 673, 675, 676, 678,680, 682, 684, 686, 688, 690, 692, 694, 695, 697, 699, 701, 702, 704,706, 708, 709, 711, 712, 713, 714, 716, 718, 720, 721, 723, 725, 726,728, 730, 732, 734, 736, 738, 740, 741, 742, 743, 744, 745, 747, 749,750, 751, 753, 755, 757, 759, 761, 762, 763, 764, 765, 767, 769, 771,773, 774, 776, 778, 779, 780, 782, 783, 784, 786, 788, 790, 792, 794,795, 796, 797, 798, 799, 800, 801, 802, 803, 804, 805, 806, 807, 808,809, 810, 811, 812, 813, 814, 815, 816, 817, 818, 819, 820, 821, 822,823, 824, 826, 827, 829, 830, 831, 832, 833, 834, 835, 837, 838, 839,840, 841, 843, 845, 847, 850, 851, 853, 855, 857, 859, 861, 862, 863,864, 865, 866, 868, 870, 872, 874, 876, 877, 879, 881, 883, 885, 887,889, 891, 893, 895, 897, 898, 900, 902, 904, 907, 909, 911, 913, 915,917, 919, 920, 922, 923, 924, 926, 928, 929, 930, 931, 932, 934, 936,937, 938, 939, 940, 941, 943, 945, 947, 948, 949, 950, 953, 955, 957,959, 961, 963, 965, 966, 967, 969, 971, 973, 975, 977, 979, 981, 983,985, 987, 989, 991, 993, 995, 997, 999, 1001, 1003, 1005, 1007, 1009,1011, 1013, 1014, 1015, 1016, 1018, 1024, 1025, 1027, 1029, 1030, 1032,1033, 1035, 1037, 1039, 1040, 1042, 1043, 1044, 1047, 1049, 1051, 1053,1055, 1057, 1059, 1061, 1063, 1065, 1067, 1068, 1069, 1071, 1072, 1073,1074, 1075, 1077, 1078, 1080, 1081, 1083, 1085, 1087, 1089, 1091, 1093,1095, 1097, 1098, 1099, 1100, 1101, 1103, 1105, 1107, 1109, 1111, 1113,1115, 1117, 1119, 1121, 1123, 1125, 1127, 1129, 1131, 1133, 1134, 1135,1136, 1137, 1138, 1139, 1141, 1143, 1145, 1147, 1149, 1151, 1153, 1155,1157, 1159, 1160, 1161, 1162, 1164, 1166, 1168, 1170, 1172, 1174, 1176,1178, 1180, 1182, 1184, 1186, 1188, 1190, 1192, 1194, 1196, 1198, 1199,1200, 1201, 1202, 1203, 1204, 1206, 1208, 1209, 1211, 1213, 1214, 1215,1216, 1217, 1219, 1221, 1223, 1225, 1227, 1229, 1230, 1232, 1234, 1236,1238, 1240, 1242, 1244, 1246, 1248, 1250, 1252, 1254, 1255, 1256, 1257,1258, 1259, 1260, 1261, 1262, 1263, 1264, 1266, 1268, 1270, 1272, 1274,1277, 1279, 1281, 1283, 1285, 1287, 1289, 1291, 1293, 1294, 1295, 1297,1298, 1299, 1301, 1303, 1305, 1307, 1309, 1311, 1313, 1315, 1317, 1319,1321, 1322, 1323, 1324, 1325, 1326, 1327, 1328, 1329, 1330, 1331, 1332,1334, 1336, 1338, 1340, 1342, 1344, 1347, 1349, 1351, 1352, 1353, 1355,1357, 1358, 1360, 1362, 1364, 1366, 1367, 1368, 1370, 1372, 1374, 1375,1377, 1379, 1381, 1383, 1385, 1387, 1389, 1391, 1393, 1395, 1397, 1399,1401, 1402, 1404, 1406, 1408, 1410, 1411, 1412, 1413, 1414, 1415, 1417,1419, 1421, 1422, 1423, 1424, 1425, 1426, 1427, 1429, 1430, 1431, 1433,1434, 1435, 1436, 1438, 1439, 1440, 1442, 1444, 1446, 1448, 1450, 1452,1457, 1458, 1460, 1462, 1464, 1466, 1467, 1468, 1469, 1471, 1473, 1475,1477, 1478, 1479, 1480, 1481, 1482, 1483, 1484, 1485, 1486, 1488, 1490,1492, 1494, 1497, 1499, 1501, 1502, 1503, 1504, 1505, 1506, 1508, 1510,1511, 1512, 1513, 1514, 1515, 1516, 1518, 1519, 1520, 1521, 1522, 1523,1524, 1525, 1527, 1528, 1529, 1531, 1532, 1533, 1534, 1535, 1536, 1540,1541, 1543, 1545, 1547, 1549, 1551, 1553, 1554, 1555, 1556, 1557, 1558,1559, 1561, 1563, 1564, 1565, 1566, 1567, 1568, 1570, 1572, 1574, 1576,1578, 1580, 1582, 1584, 1587, 1589, 1591, 1593, 1594, 1596, 1597, 1598,1599, 1600, 1601, 1602, 1603, 1604, 1605, 1606, 1607, 1609, 1611, 1612,1613, 1614, 1615, 1616, 1617, 1618, 1619, 1620, 1621, 1623, 1625, 1630,1631, 1632, 1635, 1637, 1639, 1641, 1642, 1643, 1644, 1646, 1648, 1650,1651, 1652, 1653, 1654, 1655, 1657, 1659, 1661, 1663, 1665, 1667, 1669,1671, 1673, 1675, 1677, 1679, 1681, 1682, 1684, 1686, 1688, 1690, 1692,1694, 1696, 1698, 1699, 1700, 1701, 1702, 1703, 1704, 1705, 1707, 1709,1711, 1713, 1715, 1717, 1719, 1720, 1721, 1722, 1723, 1725, 1727, 1729,1730, 1732, 1734, 1736, 1738, 1739, 1740, 1741, 1742, 1743, 1744, 1745,1746, 1748, 1750, 1751, 1752, 1754, 1756, 1758, 1760, 1762, 1764, 1766,1767, 1768, 1769, 1770, 1771, 1772, 1773, 1774, 1775, 1776, 1777, 1778,1780, 1782, 1784, 1786, 1788, 1790, 1792, 1794, 1796, 1798, 1800, 1802,1804, 1805, 1806, 1807, 1808, 1809, 1810, 1811, 1812, 1813, 1814, 1815,1816, 1817, 1818, 1819, 1820, 1821, 1822, 1823, 1824, 1825, 1826, 1827,1828, 1829, 1830, 1831, 1832, 1833, 1834, 1835, 1836, 1837, 1838, 1839,1840, 1842, 1843, 1844, 1845, 1846, 1847, 1848, 1850, 1852, 1854, 1856,1858, 1859, 1860, 1861, 1862, 1863, 1864, 1865, 1866, 1867, 1869, 1870,1871, 1873, 1875, 1877, 1879, 1881, 1883, 1885, 1887, 1889, 1891, 1893,1895, 1897, 1899, 1901, 1903, 1905, 1907, 1909, 1911, 1913, 1915, 1917,1919, 1921, 1923, 1925, 1927, 1929, 1931, 1933, 1935, 1937, 1939, 1941,1943, 1945, 1947, 1949, 1951, 1953, 1955, 1957, 1959, 1961, 1963, 1965,1967, 1969, 1971, 1973, 1975, 1977, 1979, 1981, 1983, 1985, 1987, 1989,1991, 1993, 1995, 1997, 1999, 2001, 2003, 2005, 2007, 2009, 2011, 2013,2015, 2017, 2019, 2021, 2023, 2025, 2027, 2029, 2030, 2031, 2032, 2033,2034, 2035, 2036, 2037, 2038, 2039, 2040, 2041, 2042, 2043, 2044, 2045,2046, 2047, 2048, 2049, 2050, 2051, 2052, 2053, 2054, 2055, 2056, 2057,2058, 2059, 2060, 2061, 2062, 2063, 2064, 2065, 2066, 2067, 2069, 2070,2072, 2074, 2076, 2078, 2080, 2081, 2083, 2084, 2085, 2087, 2089, 2091,2093, 2095, 2097, 2099, 2101, 2103, 2105, 2107, 2109, 2111, 2113, 2114,2115, 2116, 2117, 2118, 2119, 2120, 2121, 2123, 2125, 2127, 2129, 2131,2133, 2135, 2136, 2137, 2138, 2139, 2140, 2141, 2142, 2143, 2144, 2146,2148, 2150, 2152, 2154, 2156, 2158, 2160, 2162, 2164, 2166, 2168, 2170,2172, 2174, 2176, 2178, 2180, 2182, 2183, 2184, 2185, 2186, 2187, 2188,2189, 2190, 2191, 2192, 2193, 2194, 2195, 2196, 2197, 2198, 2199, 2200,2201, 2202, 2203, 2204, 2205, 2206, 2207, 2208, 2209, 2210, 2211, 2212,2213, 2214, 2215, 2216, 2217, 2218, 2219, 2220, 2221, 2222, 2223, 2224,2225, 2226, 2227, 2228, 2229, 2230, 2231, 2232, 2233, 2234, 2235, 2236,2237, 2238, 2239, 2240, 2241, 2242, 2243, 2244, 2245, 2246, 2247, 2248,2249, 2250, 2251, 2252, 2253, 2254, 2255, 2256, 2257, 2258, 2259, 2260,2261, 2262, 2263, 2264, 2266, 2268, 2269, 2270, 2271, 2272, 2273, 2274,2275, 2276, 2277, 2278, 2280, 2282, 2284, 2286, 2288, 2290, 2292, 2294,2296, 2298, 2300, 2302, 2304, 2306, 2308, 2310, 2312, 2314, 2316, 2318,2320, 2322, 2323, 2324, 2325, 2326, 2327, 2328, 2329, 2330, 2331, 2332,2333, 2334, 2335, 2336, 2337, 2338, 2339, 2340, 2341, 2342, 2343, 2344,2345, 2346, 2347, 2348, 2350, 2352, 2354, 2356, 2358, 2360, 2362, 2364,2366, 2368, 2370, 2372, 2374, 2375, 2376, 2377, 2378, 2379, 2380, and2381.

Also provided herein is a method of identifying whether a polymorphismis associated with variation in low light or SD+EODFR tolerance. Themethod includes the steps of: determining whether one or more geneticpolymorphisms in a population of plants is associated with the locus fora polypeptide selected from the group consisting of the polypeptidesdepicted in FIGS. 1-24 and functional homologs thereof; and measuringthe correlation between variation in the low light or SD+EODFR tolerancein plants of the population and the presence of the geneticpolymorphisms in plants of the population, thereby identifying whetheror not one or more genetic polymorphisms are associated with variationin low light or SD+EODFR tolerance. The population of plants can be apopulation of switchgrass, sorghum, sugar cane, or miscanthus plants.

A method of making a plant line is also provided herein. The methodincludes the steps of: determining whether one or more geneticpolymorphisms in a population of plants is associated with the locus fora polypeptide selected from the group consisting of the polypeptidesdepicted in FIGS. 1-24 and functional homologs thereof; identifying oneor more plants in the population in which the presence of at least oneallele at the one or more genetic polymorphisms is associated withvariation in low light or SD+EODFR tolerance; crossing each of theidentified plants with itself or a different plant to produce seed;crossing at least one progeny plant grown from the seed with itself or adifferent plant; and repeating the crossing steps for an additional 0-5generations to make the plant line, wherein the allele is present in theplant line. The population of plants can be a population of switchgrassplants.

In another aspect, this document provides a method of producing a plant.The method comprises growing a plant cell comprising an exogenousnucleic acid, wherein the exogenous nucleic acid is effective fordown-regulating an endogenous nucleic acid in the plant cell. Theendogenous nucleic acid can encode a polypeptide. The HMM bit score ofthe amino acid sequence of the polypeptide can be greater than about210. The HMM can be based on the amino acid sequences depicted in one ofFIGS. 6, 11, and 21. The plant produced from the cell can have anincrease in hypocotyl length as compared to a control plant that doesnot comprise the exogenous nucleic acid.

In another aspect, a transgenic plant cell is provided. The plant cellcomprises an exogenous nucleic acid. The exogenous nucleic acid iseffective for down-regulating an endogenous nucleic acid in the plantcell. The endogenous nucleic acid can encode a polypeptide. The HMM bitscore of the amino acid sequence of the polypeptide is greater thanabout 210. The HMM is based on the amino acid sequences depicted in oneof FIGS. 6, 11, and 21.

A transgenic plant is also provided. The transgenic plant comprises aplant cell comprising an exogenous nucleic acid. The exogenous nucleicacid is effective for down-regulating an endogenous nucleic acid in theplant cell. The endogenous nucleic acid can encode a polypeptide. TheHMM bit score of the amino acid sequence of the polypeptide is greaterthan about 210. The HMM is based on the amino acid sequences depicted inone of FIGS. 6, 11, and 21. The plant has an increase in hypocotyllength as compared to a control plant that does not comprise the plantcell.

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention pertains. Although methods and materialssimilar or equivalent to those described herein can be used to practicethe invention, suitable methods and materials are described below. Allpublications, patent applications, patents, and other referencesmentioned herein are incorporated by reference in their entirety. Incase of conflict, the present specification, including definitions, willcontrol. In addition, the materials, methods, and examples areillustrative only and not intended to be limiting.

The details of one or more embodiments of the invention are set forth inthe accompanying drawings and the description below. Other features,objects, and advantages of the invention will be apparent from thedescription and drawings, and from the claims.

DESCRIPTION OF THE DRAWINGS

FIG. 1 is an alignment of At4g37295 (Ceres Seedline ME05268; SEQ IDNO:3) with homologous and/or orthologous amino acid sequences includingCeres CLONE ID no. 1844057 (SEQ ID NO:7), Ceres ANNOT ID no. 1469148(SEQ TD NO:22), Public GI ID no. 18390998 (SEQ ID NO:25), Ceres CLONE IDno. 1065656 (SEQ ID NO:32), Ceres CLONE ID no. 1652677 (SEQ ID NO:36),Public GI ID no. 92874556 (SEQ ID NO:49), Ceres CLONE ID no. 1329161(SEQ ID NO:53), Ceres CLONE ID no. 1030378 (SEQ ID NO:55), Ceres CLONEID no. 1413787 (SEQ ID NO:57), and Public GI ID no. 125543598 (SEQ IDNO:60). In all the alignment figures shown herein, a dash in an alignedsequence represents a gap, i.e., a lack of an amino acid at thatposition. Identical amino acids or conserved amino acid substitutionsamong aligned sequences are identified by boxes. FIG. 1 and the otheralignment figures provided herein were generated using the programMUSCLE version 3.52.

FIG. 2 is an alignment of At2g32710 (Ceres Seedline ME06120; SEQ TDNO:70) with homologous and/or orthologous amino acid sequences includingCeres CLONE ID no. 1975934 (SEQ ID NO:72), Ceres ANNOT ID no. 1529913(SEQ ID NO:80), Ceres CLONE ID no. 977794 (SEQ ID NO:93), Public GI IDno. 42362378 (SEQ ID NO:96), Public GI ID no. 23899378 (SEQ ID NO:99),Public GI ID no. 15963346 (SEQ ID NO:101), Public GI ID no.15963344+B816 (SEQ ID NO:102), Public GI ID no. 92429657 (SEQ IDNO:103), Ceres CLONE ID no. 746644 (SEQ ID NO:105), Ceres CLONE ID no.623089 (SEQ ID NO:109), Ceres CLONE ID no. 1913678 (SEQ ID NO: 115), andPublic GI ID no. 115450609 (SEQ ID NO: 119).

FIG. 3 is an alignment of At2g46990 (Ceres Seedline ME09503; SEQ IDNO:129) with homologous and/or orthologous amino acid sequencesincluding Public GI ID no. 34550779 (SEQ ID NO:133), Ceres CLONE ID no.1932235 (SEQ ID NO:137), Ceres CLONE ID no. 981738 (SEQ ID NO:201),Ceres CLONE ID no. 565974 (SEQ ID NO:209), Public GI ID no. 1352058 (SEQID NO:231), Public GI ID no. 11131101 (SEQ ID NO:234), Public GI ID no.4887018 (SEQ ID NO:236), Public GI ID no. 4887018 (SEQ ID NO:236), CeresCLONE ID no. 644455 (SEQ ID NO:247), Ceres CLONE ID no. 1731500 (SEQ IDNO:270), Public GI ID no. 20269063 (SEQ ID NO:300), Public GI ID no.50404477 (SEQ ID NO:302), and Public GI ID no. 62125392 (SEQ ID NO:303).

FIG. 4 is an alignment of At4g03250 (Ceres Seedline ME10007; SEQ IDNO:317) with homologous and/or orthologous amino acid sequencesincluding Ceres CLONE ID no. 1842125 (SEQ ID NO:319), Ceres ANNOT ID no.1461360 (SEQ ID NO:321), Ceres CLONE ID no. 480906 (SEQ ID NO:327),Public GI ID no. 92889352 (SEQ ID NO:330), and Public GI ID no. 56201850(SEQ ID NO:331).

FIG. 5 is an alignment of At2g04240 (Ceres Seedline ME10852; SEQ IDNO:337), Ceres CLONE ID no. 952050 (SEQ ID NO:339) with homologousand/or orthologous amino acid sequences including Public GI ID no.115477050 (SEQ ID NO:349), Public GI ID no. 87162911 (SEQ ID NO:355),Ceres CLONE ID no. 1790901 (SEQ ID NO:357), Ceres CLONE ID no. 1460088(SEQ ID NO:370), Ceres CLONE ID no. 1734065 (SEQ ID NO:393), Ceres CLONEID no. 473509 (SEQ ID NO:395), Ceres CLONE ID no. 849918 (SEQ IDNO:401), Ceres CLONE ID no. 633470 (SEQ ID NO:409), Ceres CLONE ID no.1808334 (SEQ ID NO:417), and Ceres ANNOT ID no. 1525600 (SEQ ID NO:437).

FIG. 6 is an alignment of At5g14370 (Ceres Seedline ME11939; SEQ IDNO:456) with homologous and/or orthologous amino acid sequencesincluding Public GI ID no. 58430585 (SEQ ID NO:457), Ceres CLONE ID no.1842825 (SEQ ID NO:466), Ceres ANNOT ID no. 1449721 (SEQ ID NO:474),Public GI ID no. 41323978 (SEQ ID NO:475), Public GI ID no. 2895186 (SEQID NO:478), Public GI ID no. 22854950 (SEQ ID NO:481), Public GI ID no.116010474 (SEQ ID NO:485), Public GI ID no. 4091804 (SEQ ID NO:488),Public GI ID no. 60459257 (SEQ ID NO:494), Public GI ID no. 45544881(SEQ ID NO:496), Public GI ID no. 36789802 (SEQ ID NO:498), Public GI LDno. 92875402 (SEQ ID NO:508), Public GI ID no. 118406898 (SEQ IDNO:510), Public GI ID no. 107770485 (SEQ ID NO:511), Public GI ID no.21655154 (SEQ ID NO:532), Public GI ID no. 90657642 (SEQ ID NO:536), andCeres CLONE ID no. 1569555 (SEQ ID NO:1842).

FIG. 7 is an alignment of At1g70270 (Ceres Seedline ME13456; SEQ IDNO:634) with homologous and/or orthologous amino acid sequencesincluding Public GI ID no. 98961985 (SEQ ID NO:637).

FIG. 8 is an alignment of At4g25480 (Ceres Seedline ME15935; SEQ IDNO:644) with homologous and/or orthologous amino acid sequencesincluding SEQ ID NO:645, Ceres CLONE ID no. 1849479 (SEQ ID NO:767),Public GI ID no. 89275008 (SEQ ID NO:796), Public GI ID no. 120400525(SEQ ID NO:797), Public GI ID no. 98980426 (SEQ ID NO:804), Public GI IDno. 71983373 (SEQ ID NO:808), Public GI ID no. 41351817 (SEQ ID NO:809),Public GI ID no. 76446191 (SEQ ID NO:811), Public GI ID no. 5616086 (SEQID NO:813), Ceres CLONE ID no. 1052602 (SEQ ID NO:826), Public GI ID no.72068957 (SEQ ID NO:830), Public GI ID no. 71534113 (SEQ ID NO:831),Public GI ID no. 37147896 (SEQ ID NO:832), Public GI ID no. 92918850(SEQ ID NO:834), Public GI ID no. 40647095 (SEQ ID NO:835), Ceres ANNOTID no. 1527711 (SEQ ID NO:837), Public GI ID no. 71041116 (SEQ IDNO:838). Public GI ID no. 12003384 (SEQ ID NO:839), Public GI ID no.18535580 (SEQ ID NO:840), and Public GI ID no. 115353971 (SEQ IDNO:1843).

FIG. 9 is an alignment of At2g33780 (Ceres SEEDLINE ID no. ME16594, SEQID NO:850) with homologous and/or orthologous amino acid sequencesincluding Ceres CLONE ID no. 1833093 (SEQ ID NO:853), Ceres ANNOT ID no.1502190 (SEQ ID NO:857), Ceres CLONE ID no. 565641 (SEQ ID NO:876),Public GI ID no. 87240507 (SEQ ID NO:877), Ceres CLONE ID no. 1325382(SEQ ID NO:881), Ceres CLONE ID no. 1558265 (SEQ ID NO:885), Ceres CLONETD no. 1823669 (SEQ ID NO:895), and Public GI ID no. 115464921 (SEQ IDNO:898).

FIG. 10 is an alignment of At4g17810 (Ceres SEEDLINE ID no. ME16597, SEQID NO:907) with homologous and/or orthologous amino acid sequencesincluding Ceres CLONE ID no. 1940797 (SEQ ID NO:909), Ceres ANNOT ID no.1538900 (SEQ ID NO:911), Ceres CLONE ID no. 1126868 (SEQ ID NO:922),Public GI ID no. 89257684 (SEQ ID NO:923), Public GI ID no. 124360460(SEQ ID NO:929), Public GI ID no. 62865694 (SEQ ID NO:931), Public GI IDno. 62865692 (SEQ ID NO:932), Ceres CLONE ID no. 260368 (SEQ ID NO:936),Ceres CLONE ID no. 1873510 (SEQ ID NO:947), Public GI ID no. 125541662(SEQ ID NO:948), Public GI ID no. 48716268 (SEQ ID NO:950), and PublicGI ID no. 62865696 (SEQ ID NO:1844).

FIG. 11 is an alignment of At1g13360 (Ceres SEEDLINE ID no. ME16630, SEQID NO:953) with homologous and/or orthologous amino acid sequencesincluding Ceres CLONE ID no. 1798705 (SEQ ID NO:955), Ceres ANNOT ID no.1458907 (SEQ ID NO:963), Ceres CLONE ID no. 1090409 (SEQ ID NO:971),Ceres CLONE ID no. 479817 (SEQ ID NO:977), Ceres CLONE ID no. 1041793(SEQ ID NO:979), Ceres CLONE ID no. 684633 (SEQ ID NO:985), Ceres CLONEID no. 371815 (SEQ ID NO:991), Ceres CLONE ID no. 1686460 (SEQ IDNO:993), Ceres CLONE ID no. 1448595 (SEQ ID NO:995), Ceres CLONE ID no.1734477 (SEQ ID NO:999), Ceres CLONE ID no. 1605693 (SEQ ID NO:1005),Ceres CLONE ID no. 1757400 (SEQ ID NO:1009), and Public GI ID no.115434334 (SEQ ID NO:1015).

FIG. 12 is an alignment of At1g75860 (Ceres SEEDLINE ID no. ME17128, SEQID NO:1024) with homologous and/or orthologous amino acid sequencesincluding Ceres ANNOT ID no. 1452905 (SEQ ID NO:1029), Ceres CLONE IDno. 956176 (SEQ ID NO:1039), Public GI ID no. 92870366 (SEQ ID NO:1040),Ceres CLONE ID no. 294166 (SEQ ID NO:1042), and Public GI ID no.125543067 (SEQ ID NO:1043).

FIG. 13 is an alignment of At4g19700 (Ceres SEEDLINE ID no. ME17578, SEQID NO:1047) with homologous and/or orthologous amino acid sequencesincluding Ceres CLONE ID no. 1837694 (SEQ ID NO:1053), Ceres ANNOT IDno. 1483367 (SEQ ID NO:1057), Ceres CLONE ID no. 1077781 (SEQ IDNO:1083), Ceres CLONE ID no. 471026 (SEQ ID NO:1085), Public GI ID no.92888885 (SEQ ID NO:1099), Public GI ID no. 45544873 (SEQ ID NO: 1100),Public GI ID no. 45758663 (SEQ ID NO:1101), Ceres CLONE ID no. 772927(SEQ ID NO: 1105), Ceres CLONE ID no. 895080 (SEQ ID NO:1111), CeresCLONE ID no. 1806128 (SEQ ID NO:1131), Public GI ID no. 115458192 (SEQID NO: 1134), and Public GI ID no. 82470795 (SEQ ID NO:1139).

FIG. 14 is an alignment of At1g58100 (Ceres SEEDLINE ID no. ME18158, SEQID NO:1151) with homologous and/or orthologous amino acid sequencesincluding Ceres CLONE ID no. 1851526 (SEQ ID NO: 1155), Ceres ANNOT IDno. 1486769 (SEQ ID NO:1172), Public GI ID no. 83032232 (SEQ IDNO:1209), Ceres CLONE ID no. 1620420 (SEQ ID NO:1211), Public GI ID no.92892428 (SEQ ID NO:1215), Ceres CLONE ID no. 884742 (SEQ ID NO:1223),Ceres CLONE ID no. 1821559 (SEQ ID NO:1246), Public GI ID no. 51535021(SEQ ID NO:1258), Public GI ID no. 113205304 (SEQ ID NO:1263), andPublic GI ID no. 37719051 (SEQ ID NO:1264).

FIG. 15 is an alignment of At5g46170 (Ceres SEEDLINE ID no. ME18314, SEQID NO:1277) with homologous and/or orthologous amino acid sequencesincluding Ceres CLONE ID no. 1926352 (SEQ ID NO:1279), Ceres ANNOT IDno. 1448905 (SEQ ID NO:1285), Public GI ID no. 15236865 (SEQ IDNO:1294), Ceres CLONE ID no. 934771 (SEQ ID NO:1301), Ceres CLONE ID no.338386 (SEQ ID NO:1303), Ceres CLONE ID no. 1780691 (SEQ ID NO:1317),and Public GI ID no. 115464819 (SEQ ID NO:1326).

FIG. 16 is an alignment of At4g32280 (Ceres SEEDLINE ID no. ME18408, SEQID NO:1347) with homologous and/or orthologous amino acid sequencesincluding Ceres CLONE ID no. 285028 (SEQ ID NO:1419), Ceres CLONE ID no.100969565 (SEQ ID NO:1422), Public GI ID no. 1352057 (SEQ ID NO:1427),Ceres ANNOT ID no. 1453784 (SEQ ID NO:1429), Public GI ID no. 452777(SEQ ID NO:1430), and Public GI ID no. 92873297 (SEQ ID NO:1431).

FIG. 17 is an alignment of At3g02830 (Ceres SEEDLINE ID no. ME19304, SEQID NO:1457) with homologous and/or orthologous amino acid sequencesincluding Ceres CLONE ID no. 1924904 (SEQ ID NO:1460), Ceres ANNOT IDno. 1543346 (SEQ ID NO:1462), Public GI ID no. 18396338 (SEQ IDNO:1467), Ceres CLONE ID no. 833872 (SEQ ID NO:1471), Ceres CLONE ID no.1579587 (SEQ ID NO:1475), Ceres CLONE ID no. 1786411 (SEQ ID NO:1477),and Public GI ID no. 108864370 (SEQ ID NO:1480).

FIG. 18 is an alignment of At4g08920 (Ceres SEEDLINE ID no. ME19738, SEQID NO:1497) with homologous and/or orthologous amino acid sequencesincluding Ceres ANNOT ID no. 1443463 (SEQ ID NO:1499), Public GI ID no.13605525 (SEQ ID NO:1502). Public GI ID no. 94965681 (SEQ ID NO:1506),and Public GI ID no. 28201254 (SEQ ID NO:1512).

FIG. 19 is an alignment of At4g11660 (Ceres SEEDLINE ID no. ME20871, SEQID NO:1587) with homologous and/or orthologous amino acid sequencesincluding Ceres CLONE ID no. 1839577 (SEQ ID NO:1589), Ceres ANNOT IDno. 1491567 (SEQ ID NO:1591), Ceres CLONE ID no. 574505 (SEQ IDNO:1596), Public GI ID no. 56117815 (SEQ ID NO:1597), Public GI ID no.92874021 (SEQ ID NO:1603), Public GI ID no. 123684 (SEQ ID NO:1605),Public GI ID no. 5821136 (SEQ ID NO:1606), Ceres CLONE ID no. 283366(SEQ ID NO:1609), Public GI ID no. 16118447 (SEQ ID NO:1612), and PublicGI ID no. 125562434 (SEQ ID NO:1614).

FIG. 20 is an alignment of At2g45700 (Ceres SEEDLINE ID no. ME21508, SEQID NO:1635) with homologous and/or orthologous amino acid sequencesincluding Ceres ANNOT ID no. 1508307 (SEQ ID NO:1637), Public GI ID no.1495267 (SEQ ID NO:1642), Public GI ID no. 87241310 (SEQ ID NO:1644),Ceres CLONE ID no. 938390 (SEQ ID NO:1646), Ceres CLONE ID no. 272338(SEQ ID NO:1648), Ceres CLONE ID no. 1993510 (SEQ ID NO:1650), Public GIID no. 125563862 (SEQ ID NO:1651), and Public GI ID no. 125605833 (SEQID NO:1653).

FIG. 21 is an alignment of At2g35940 (Ceres SEEDLINE ID no. ME19971, SEQID NO:1540) with homologous and/or orthologous amino acid sequencesincluding Ceres CLONE ID no. 1943265 (SEQ ID NO:1543), Ceres ANNOT IDno. 1454522 (SEQ ID NO:1547), Public GI ID no. 31323447 (SEQ IDNO:1556), Ceres CLONE ID no. 1583941 (SEQ ID NO:1561), Ceres CLONE IDno. 1792942 (SEQ ID NO:1563), Public GI ID no. 77548772 (SEQ IDNO:1565), and Public GI ID no. 84453182 (SEQ ID NO:1567).

FIG. 22 is an alignment of At1g04400 (Ceres SEEDLINE ID no. ME12006, SEQID NO:538) with homologous and/or orthologous amino acid sequencesincluding Public GI ID no. 5731739 (SEQ ID NO:539), Ceres ANNOT ID no.1538045 (SEQ ID NO:541), Public GI ID no. 29467479 (SEQ ID NO:542),Public GI ID no. 133921974 (SEQ ID NO:543), Public GI ID no. 113197027(SEQ ID NO:544), Public GI ID no. 92879277 (SEQ ID NO:545), Public GI IDno. 45935260 (SEQ ID NO:546), Public GI ID no. 8101444 (SEQ ID NO:547),Public GI ID no. 78217443 (SEQ ID NO:548), and Public GI ID no. 28372347(SEQ ID NO:549).

FIG. 23 is an alignment of At3g45610 (Ceres SEEDLINE ID no. ME12899, SEQID NO:606) with homologous and/or orthologous amino acid sequencesincluding Public GI ID no. 92873064 (SEQ ID NO:607), Public GI ID no.37051125 (SEQ ID NO:608), and Public GI ID no. 112363376 (SEQ IDNO:609).

FIG. 24 is an alignment of At4g08330 (Ceres SEEDLINE ID no. ME12596, SEQID NO:570) with homologous and/or orthologous amino acid sequencesincluding Ceres CLONE ID no. 1919714 (SEQ ID NO:572), Ceres ANNOT ID no.1443290 (SEQ ID NO:574), Ceres CLONE ID no. 1042157 (SEQ ID NO:576),Ceres CLONE ID no. 1384304 (SEQ ID NO:578), and Public GI ID no.115464375 (SEQ ID NO:579).

DETAILED DESCRIPTION

This document provides methods and materials related to modulatingtolerance of plants to Short Day plus End-of-Day Far-Red (SD+EODFR)conditions or low light irradiation. In some embodiments, the plants mayhave increased SD+EODFR tolerance and increased low light tolerance. Themethods can include transforming a plant cell with a nucleic acidencoding an SD+EODFR and/or low light-tolerance polypeptide, whereinexpression of the polypeptide results in increased SD+EODFR and/or lowlight tolerance. Plant cells produced using such methods can be grown toproduce plants having an increased SD+EODFR and/or low light tolerance.Such plants can also be used to produce crops, plant products, biomass,and/or nitrogen fixating plants in shady or low light areas, such asunder the canopy of another crop. For example, the methods and materialsprovided herein can be used to produce a legume (a member of Fabaceae,e.g., peas, beans, lupins, lentils, chick peas, vethes, soybeans,clovers, alfalfas, and peanuts) having an increased SD+EODFR and/or lowlight tolerance and which can be grown under the canopy of a taller crop(e.g., corn, switchgrass, sorghum, sugar cane, or miscanthus). In otherembodiments, the taller plant is a nitrogen fixating plant (e.g., amember of Fabaceae, such as tamarind, mimosa, acacia, and carob) and theSD+EODFR and/or low light tolerant plant is a shorter plant, such ascorn, switchgrass, sorghum, sugar cane, or miscanthus.

I. DEFINITIONS

“Amino acid” refers to one of the twenty biologically occurring aminoacids and to synthetic amino acids, including D/L optical isomers.

“Cell type-preferential promoter” or “tissue-preferential promoter”refers to a promoter that drives expression preferentially in a targetcell type or tissue, respectively, but may also lead to sometranscription in other cell types or tissues as well.

“Control plant” refers to a plant that does not contain the exogenousnucleic acid present in a transgenic plant of interest, but otherwisehas the same or similar genetic background as such a transgenic plant. Asuitable control plant can be a non-transgenic wild type plant, anon-transgenic segregant from a transformation experiment, or atransgenic plant that contains an exogenous nucleic acid other than theexogenous nucleic acid of interest.

“Domains” are groups of substantially contiguous amino acids in apolypeptide that can be used to characterize protein families and/orparts of proteins. Such domains have a “fingerprint” or “signature” thatcan comprise conserved primary sequence, secondary structure, and/orthree-dimensional conformation. Generally, domains are correlated withspecific in vitro and/or in vivo activities. A domain can have a lengthof from 10 amino acids to 400 amino acids, e.g., 10 to 50 amino acids,or 25 to 100 amino acids, or 35 to 65 amino acids, or 35 to 55 aminoacids, or 45 to 60 amino acids, or 200 to 300 amino acids, or 300 to 400amino acids.

“Down-regulation” refers to regulation that decreases the level of anexpression product (mRNA, polypeptide, or both) relative to basal ornative states.

“Exogenous” with respect to a nucleic acid indicates that the nucleicacid is part of a recombinant nucleic acid construct, or is not in itsnatural environment. For example, an exogenous nucleic acid can be asequence from one species introduced into another species, i.e., aheterologous nucleic acid. Typically, such an exogenous nucleic acid isintroduced into the other species via a recombinant nucleic acidconstruct. An exogenous nucleic acid can also be a sequence that isnative to an organism and that has been reintroduced into cells of thatorganism. An exogenous nucleic acid that includes a native sequence canoften be distinguished from the naturally occurring sequence by thepresence of non-natural sequences linked to the exogenous nucleic acid,e.g., non-native regulatory sequences flanking a native sequence in arecombinant nucleic acid construct. In addition, stably transformedexogenous nucleic acids typically are integrated at positions other thanthe position where the native sequence is found. It will be appreciatedthat an exogenous nucleic acid may have been introduced into aprogenitor and not into the cell under consideration. For example, atransgenic plant containing an exogenous nucleic acid can be the progenyof a cross between a stably transformed plant and a non-transgenicplant. Such progeny are considered to contain the exogenous nucleicacid.

“Expression” refers to the process of converting genetic information ofa polynucleotide into RNA through transcription, which is catalyzed byan enzyme. RNA polymerase, and into protein, through translation of mRNAon ribosomes.

“Heterologous polypeptide” as used herein refers to a polypeptide thatis not a naturally occurring polypeptide in a plant cell, e.g., atransgenic Panicum virgatum plant transformed with and expressing thecoding sequence for a nitrogen transporter polypeptide from a Zea maysplant.

“Isolated nucleic acid” as used herein includes a naturally-occurringnucleic acid, provided one or both of the sequences immediately flankingthat nucleic acid in its naturally-occurring genome is removed orabsent. Thus, an isolated nucleic acid includes, without limitation, anucleic acid that exists as a purified molecule or a nucleic acidmolecule that is incorporated into a vector or a virus. A nucleic acidexisting among hundreds to millions of other nucleic acids within, forexample, cDNA libraries, genomic libraries, or gel slices containing agenomic DNA restriction digest, is not to be considered an isolatednucleic acid.

“Modulation” of the level of tolerance to a stimulus (e.g., low lightconditions or SD+EODFR conditions) refers to the change in the level oftolerance of the indicated stimulus that is observed as a result ofexpression of, or transcription from, an exogenous nucleic acid in aplant cell. The change in level is measured relative to thecorresponding level in control plants.

“Nucleic acid” and “polynucleotide” are used interchangeably herein, andrefer to both RNA and DNA, including cDNA, genomic DNA, synthetic DNA,and DNA or RNA containing nucleic acid analogs. Polynucleotides can haveany three-dimensional structure. A nucleic acid can be double-strandedor single-stranded (i.e., a sense strand or an antisense strand).Non-limiting examples of polynucleotides include genes, gene fragments,exons, introns, messenger RNA (mRNA), transfer RNA, ribosomal RNA,siRNA, micro-RNA, ribozymes, cDNA, recombinant polynucleotides, branchedpolynucleotides, nucleic acid probes and nucleic acid primers. Apolynucleotide may contain unconventional or modified nucleotides.

“Operably linked” refers to the positioning of a regulatory region and asequence to be transcribed in a nucleic acid so that the regulatoryregion is effective for regulating transcription or translation of thesequence. For example, to operably link a coding sequence and aregulatory region, the translation initiation site of the translationalreading frame of the coding sequence is typically positioned between oneand about fifty nucleotides downstream of the regulatory region. Aregulatory region can, however, be positioned as much as about 5,000nucleotides upstream of the translation initiation site, or about 2,000nucleotides upstream of the transcription start site.

“Polypeptide” as used herein refers to a compound of two or more subunitamino acids, amino acid analogs, or other peptidomimetics, regardless ofpost-translational modification, e.g., phosphorylation or glycosylation.The subunits may be linked by peptide bonds or other bonds such as, forexample, ester or ether bonds. Full-length polypeptides, truncatedpolypeptides, point mutants, insertion mutants, splice variants,chimeric proteins, and fragments thereof are encompassed by thisdefinition.

“Progeny” includes descendants of a particular plant or plant line.Progeny of an instant plant include seeds formed on F₁, F₂, F₃, F₄, F₅,F₆ and subsequent generation plants, or seeds formed on BC₁, BC₂, BC₃,and subsequent generation plants, or seeds formed on F₁BC₁, F₁BC₂,F₁BC₃, and subsequent generation plants. The designation F₁ refers tothe progeny of a cross between two parents that are geneticallydistinct. The designations F₂, F₃, F₄, F₅ and F₆ refer to subsequentgenerations of self- or sib-pollinated progeny of an F_(t) plant.

“Regulatory region” refers to a nucleic acid having nucleotide sequencesthat influence transcription or translation initiation and rate, andstability and/or mobility of a transcription or translation product.Regulatory regions include, without limitation, promoter sequences,enhancer sequences, response elements, protein recognition sites,inducible elements, protein binding sequences, 5′ and 3′ untranslatedregions (UTRs), transcriptional start sites, termination sequences,polyadenylation sequences, introns, and combinations thereof. Aregulatory region typically comprises at least a core (basal) promoter.A regulatory region also may include at least one control element, suchas an enhancer sequence, an upstream element or an upstream activationregion (UAR). For example, a suitable enhancer is a cis-regulatoryelement (−212 to −154) from the upstream region of the octopine synthase(ocs) gene. Fromm et al., The Plant Cell, 1:977-984 (1989).

“Up-regulation” refers to regulation that increases the level of anexpression product (mRNA, polypeptide, or both) relative to basal ornative states.

“Vector” refers to a replicon, such as a plasmid, phage, or cosmid, intowhich another DNA segment may be inserted so as to bring about thereplication of the inserted segment. Generally, a vector is capable ofreplication when associated with the proper control elements. The term“vector” includes cloning and expression vectors, as well as viralvectors and integrating vectors. An “expression vector” is a vector thatincludes a regulatory region.

II. POLYPEPTIDES

Polypeptides described herein include SD+EODFR and/or low lighttolerancepolypeptides. SD+EODFR and/or low light tolerance polypeptidescan be effective to increase SD+EODFR and/or low light tolerance whenexpressed in a plant or plant cell. Such polypeptides typically containat least one domain indicative of SD+EODFR and/or low light tolerancepolypeptides, as described in more detail herein. SD+EODFR and/or lowlight tolerance polypeptides typically have an HMM bit score that isgreater than 20 for an HMM model based on one of the alignments setforth in FIGS. 1-24, as described in more detail herein. In someembodiments, SD+EODFR and/or low light tolerance polypeptides havegreater than 40% identity to SEQ ID NO:3, SEQ ID NO:70, SEQ ID NO:129,SEQ ID NO:317, SEQ ID NO:337, SEQ ID NO:456, SEQ ID NO:538, SEQ IDNO:570, SEQ ID NO:606, SEQ ID NO:634, SEQ ID NO:644, SEQ ID NO:850, SEQID NO:907, SEQ ID NO:953, SEQ ID NO:1024, SEQ ID NO:1047, SEQ IDNO:1151, SEQ ID NO:1277. SEQ ID NO:1347, SEQ ID NO:1457, SEQ ID NO:1497,SEQ ID NO:1540, SEQ ID NO:1587, SEQ ID NO:1630, or SEQ ID NO:1635 asdescribed in more detail herein.

Polypeptides described herein include red light specific responsepathway polypeptides. Red light specific response pathway polypeptidescan be effective to decrease hypocotyl length when over-expressed in aplant or plant cell. Such polypeptides typically contain at least onedomain indicative of red light specific response pathway polypeptides,as described in more detail herein. Red light specific response pathwaypolypeptides typically have an HMM bit score that is greater than 20 foran HMM model based on one of the alignments set forth in FIGS. 6, 11,and 24, as described in more detail herein. In some embodiments, redlight specific response pathway polypeptides have greater than 40%identity to SEQ ID NO:456, SEQ ID NO:953, or SEQ ID NO:1540 as describedin more detail herein.

A. Domains Indicative of SD+EODFR and/or Low Light TolerancePolypeptides

A low light tolerance polypeptide can contain a cyclin dependent kinaseinhibitor (CDI) domain. Cell cycle progression is negatively controlledby cyclin-dependent kinases inhibitor (CDIs). CDIs are involved in cellcycle arrest at the G1 phase. The motif is also present in SEQ ID NO:70,which sets forth the amino acid sequence of an Arabidopsis clone,identified herein as At2g32710 (SEQ ID NO:69), that is predicted toencode a cyclin-dependent kinase inhibitor 4 (KIP4) polypeptide.

A low light tolerance polypeptide can contain an AUX/IAA domain, whichis predicted to be characteristic of an Aux/IAA transcriptionalrepressor. AUX/IAA proteins act as repressors of auxin-induced geneexpression, possibly through modulating the activity of DNA-bindingauxin response factors (ARFs). SEQ ID NO:129 sets forth the amino acidsequence of an Arabidopsis clone, identified herein as At2g46990 (SEQ IDNO:127), that is predicted to encode an auxin-induced IAA21 polypeptide.An SD+EODFR tolerance and low light tolerance polypeptide can alsocontain an AUX/IAA domain. SEQ ID NO:1347 sets forth the amino acidsequence of an Arabidopsis clone, identified herein as At1g32280 (SEQ IDNO:1345), that is predicted to encode an auxin-responsive IAA29polypeptide containing an AUX/IAA domain.

A low light tolerance polypeptide can contain a homeobox domain.Homeobox domains bind DNA through a helix-turn-helix (HTH) structure.The HTH motif is characterised by two alpha-helices, which make intimatecontacts with the DNA and are joined by a short turn. The second helixbinds to DNA via a number of hydrogen bonds and hydrophobicinteractions, which occur between specific side chains and the exposedbases and thymine methyl groups within the major groove of the DNA. Thefirst helix helps to stabilise the structure. SEQ ID NO:317 sets forththe amino acid sequence of an Arabidopsis clone, identified herein asAt4g03250 (SEQ ID NO:315), that is predicted to encode a polypeptidecontaining a homeobox domain.

A low light tolerance polypeptide can contain a C3HC4 type zinc-finger(zf_C3HC4) domain. The C3HC4 type zinc-finger (RING finger) is acysteine-rich domain of 40 to 60 residues that coordinates two zincions, and has the consensus sequence:C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is anyamino acid. Many proteins containing a RING finger play a role in theubiquitination pathway. SEQ ID NO:337 sets forth the amino acid sequenceof an Arabidopsis clone, identified herein as At2g04240 (SEQ ID NO:335),that is predicted to encode a polypeptide containing zf_C3HC4 domain.

A low light tolerance polypeptide can contain a B-box zinc finger(zf-B_box) domain and a CCT motif. A B-box zinc finger domain is about40 amino acids in length. One or two copies of this domain are generallyassociated with a ring finger and a coiled coil motif. B-box zinc fingerdomains are found in transcription factors, ribonucleoproteins andprotooncoproteins, but no function is clearly assigned. The CCT(CONSTANS, CO-like, and TOC1) motif is a highly conserved basic domainof about 43 amino acids, and is found near the C-terminus of plantproteins often involved in light signal transduction. The CCT motif isfound in association with other domains, such as B-box zinc fingerdomains, GATA-type zinc finger domains, ZIM motifs, or responseregulatory domains. The CCT motif contains a putative nuclearlocalization signal within the second half of the CCT motif, has beenshown to be involved in nuclear localization, and likely has a role inprotein-protein interaction. SEQ ID NO:456 sets forth the amino acidsequence of an Arabidopsis clone, identified herein as At5g14370 (SEQ IDNO:454), that is predicted to encode a polypeptide containing a B-boxzinc finger domain and a CCT motif.

An SD+EODFR tolerance polypeptide can contain a DNA photolyase domainand a FAD_binding_7 domain (FAD binding domain of DNA photolyase). DNAphotolyases are enzymes that repair mismatched pyrimidine dimers in DNAthat are induced by exposure to ultra-violet light. Proteins containinga FAD_binding_7 domain include Arabidopsis cryptochromes 1 (CRY1) and 2(CRY2), which are blue light photoreceptors that mediate bluelight-induced gene expression. SEQ ID NO:538 sets forth the amino acidsequence of an Arabidopsis clone, identified herein as At1g04400 (SEQ IDNO:537), that is predicted to encode a cryptochrome 2 apoproteinpolypeptide containing a FAD_binding_7 domain and a DNA photolyasedomain. A low light-tolerance polypeptide can also FAD_binding_7 domainand a DNA photolyase domain. SEQ ID NO:1497 sets forth the amino acidsequence of an Arabidopsis clone, identified herein as At4g08920 (SEQ IDNO:1496), that is predicted to encode a cryptochrome 1 (CRY1),flavin-type blue-light photoreceptor apoprotein polypeptide containing aFAD_binding_7 domain and a DNA photolyase domain.

An SD+EODFR tolerance polypeptide can contain a zf_Dof domain, which ispredicted to be characteristic of a Dof domain zinc finger polypeptide.SEQ ID NO:606 sets forth the amino acid sequence of an Arabidopsisclone, identified herein as At3g45610 (SEQ ID NO:605), that is predictedto encode a polypeptide containing a zf_Dof domain.

A low light tolerance polypeptide can contain an AP2 domain, which ispredicted to be characteristic of an ERF/AP2 transcription factor. AP2domains are typically about 60 amino acid residues in length. SEQ IDNO:645 sets forth the amino acid sequence of an Arabidopsis clone,identified herein as At4g25480 (SEQ ID NO:642), that is predicted toencode a DREB subfamily A-1 polypeptide of the ERF/AP2 transcriptionfactor family containing an AP2 domain.

A low light tolerance polypeptide can contain a VQ motif. VQ motifs areshort conserved motifs of FXhVQChTG, where X is any amino acid and h isa hydrophobic amino acid, that is found in a variety of plant proteins.SEQ ID NO:850 sets forth the amino acid sequence of an Arabidopsisclone, identified herein as At2g33780 (SEQ ID NO:848), that is predictedto encode a polypeptide containing a VQ motif.

A low light tolerance polypeptide can contain a zf_C2H2 domain, which ispredicted to be characteristic of a C2H2-type zinc finger. C2H2 zincfingers are composed of two short beta strands followed by an alphahelix. The amino terminal part of the helix binds the major groove ofDNA. The two conserved cysteines and histidines of a C2H2 zinc fingerdomain coordinate a zinc ion. SEQ ID NO:907 sets forth the amino acidsequence of an Arabidopsis clone, identified herein as At4g17810 (SEQ IDNO:905), that is predicted to encode a polypeptide containing a zf_C2H2domain.

A low light tolerance polypeptide can contain a TCP domain, which ispredicted to be characteristic of a TCP family transcription factor. TheTCP family of transcription factors is named after its firstcharacterized members, TB1, CYC and PCF1 and PCF2. TCP domains arepredicted to form non-canonical basic-Helix-Loop-Helix (bHLP)structures. The TCP domains found in two rice DNA-binding proteins, PCF1and PCF2, have been shown to be involved in DNA-binding anddimerization. SEQ ID NO:1151 sets forth the amino acid sequence of anArabidopsis clone, identified herein as At1g58100 (SEQ ID NO:1150), thatis predicted to encode a polypeptide containing a TCP domain.

A low light tolerance polypeptide can contain an F-box domain. F-boxdomains have a role in mediating protein-protein interactions in avariety of contexts, such as polyubiquitination, transcriptionelongation, centromeric binding and translational repression. Two motifsthat are commonly found associated with F-box domains are leucine richrepeats and WD repeats. SEQ ID NO:1277 sets forth the amino acidsequence of an Arabidopsis clone, identified herein as At5g46170 (SEQ IDNO:1276), that is predicted to encode a polypeptide containing an F-boxdomain.

A low light tolerance polypeptide can contain a zf_CCCH domain, which ispredicted to be characteristic of a C-x8-C-x5-C-x3-H type zinc fingerpolypeptide. The zf-CCCH domain is often found associated with proteinsthat interact with the 3′ untranslated region of various mRNAs. SEQ IDNO:1457 sets forth the amino acid sequence of an Arabidopsis clone,identified herein as At3g02830 (SEQ ID NO:1456), that is predicted toencode a polypeptide containing a zf_CCCH domain.

An SD+EODFR tolerance and low light tolerance polypeptide can contain aPOX domain and a homeobox domain. POX domains are often found in plantproteins with a homeobox domain, indicating that such proteins arelikely transcription factors. SEQ ID NO:1540 sets forth the amino acidsequence of an Arabidopsis clone, identified herein as At2g35940 (SEQ IDNO:1537), that is predicted to encode a BEL1-like homeodomain 1polypeptide containing a POX domain and a homeobox domain.

A low light tolerance polypeptide can contain an HSF-type DNA-bindingdomain, which is predicted to be characteristic of heat shock factortranscription activator. Heat shock factor transcription activators areoften found associated with heat shock protein promoters during heatshock. SEQ ID NO:1587 sets forth the amino acid sequence of anArabidopsis clone, identified herein as At4g11660 (SEQ ID NO:1586), thatis predicted to encode a polypeptide containing an HSF-type DNA-bindingdomain.

A low light tolerance polypeptide can contain a sterile alpha motif(SAM_1) domain and a DNA repair metallo-beta-lactamase (DRMBL) domain,which is predicted to be characteristic of a DNA repairmetallo-beta-lactamase. SEQ ID NO:1635 sets forth the amino acidsequence of an Arabidopsis clone, identified herein as Ceres At2g45700(SEQ ID NO:1634), that is predicted to encode a polypeptide containing aSAM domain and a DRMBL domain.

B. Domains Indicative of Red Light Specific Response PathwayPolypeptides

A red light specific response pathway polypeptide can contain a B-boxzinc finger (zf-B_box) domain and a CCT motif. A B-box zinc fingerdomain is about 40 amino acids in length. One or two copies of thisdomain are generally associated with a ring finger and a coiled coilmotif. B-box zinc finger domains are found in transcription factors,ribonucleoproteins and protooncoproteins, but no function is clearlyassigned. The CCT (CONSTANS, CO-like, and TOC1) motif is a highlyconserved basic domain of about 43 amino acids, and is found near theC-terminus of plant proteins often involved in light signaltransduction. The CCT motif is found in association with other domains,such as B-box zinc finger domains, GATA-type zinc finger domains, ZIMmotifs, or response regulatory domains. The CCT motif contains aputative nuclear localization signal within the second half of the CCTmotif, has been shown to be involved in nuclear localization, and likelyhas a role in protein-protein interaction. SEQ ID NO:456 sets forth theamino acid sequence of an Arabidopsis clone, identified herein asAt5g14370 (SEQ ID NO:454), that is predicted to encode a polypeptidecontaining a B-box zinc finger domain and a CCT motif.

A red light specific response pathway polypeptide can contain a POXdomain and a homeobox domain. POX domains are often found in plantproteins with a homeobox domain, indicating that such proteins arelikely transcription factors. SEQ ID NO:1540 sets forth the amino acidsequence of an Arabidopsis clone, identified herein as At2g35940 (SEQ IDNO:1537), that is predicted to encode a BEL1-like homeodomain 1polypeptide containing a POX domain and a homeobox domain.

C. Functional Homologs Identified by Reciprocal BLAST

In some embodiments, one or more functional homologs of a referenceSD+EODFR and/or low light tolerance polypeptide defined by one or moreof the pfam descriptions indicated above are suitable for use asSD+EODFR and/or low light tolerance polypeptides. A functional homologis a polypeptide that has sequence similarity to a referencepolypeptide, and that carries out one or more of the biochemical orphysiological function(s) of the reference polypeptide. A functionalhomolog and the reference polypeptide may be natural occurringpolypeptides, and the sequence similarity may be due to convergent ordivergent evolutionary events. As such, functional homologs aresometimes designated in the literature as homologs, or orthologs, orparalogs. Variants of a naturally occurring functional homolog, such aspolypeptides encoded by mutants of a wild type coding sequence, maythemselves be functional homologs. Functional homologs can also becreated via site-directed mutagenesis of the coding sequence for anSD+EODFR and/or low light tolerance polypeptide, or by combining domainsfrom the coding sequences for different naturally-occurring SD+EODFRand/or low light tolerance polypeptides (“domain swapping”). The term“functional homolog” is sometimes applied to the nucleic acid thatencodes a functionally homologous polypeptide.

Functional homologs can be identified by analysis of nucleotide andpolypeptide sequence alignments. For example, performing a query on adatabase of nucleotide or polypeptide sequences can identify homologs ofSD+EODFR and/or low light tolerance polypeptides. Sequence analysis caninvolve BLAST, Reciprocal BLAST, or PSI-BLAST analysis of nonredundantdatabases using an SD+EODFR and/or low light tolerance polypeptide aminoacid sequence as the reference sequence. Amino acid sequence is, in someinstances, deduced from the nucleotide sequence. Those polypeptides inthe database that have greater than 40% sequence identity are candidatesfor further evaluation for suitability as an SD+EODFR and/or low lighttolerance polypeptide. Amino acid sequence similarity allows forconservative amino acid substitutions, such as substitution of onehydrophobic residue for another or substitution of one polar residue foranother. If desired, manual inspection of such candidates can be carriedout in order to narrow the number of candidates to be further evaluated.Manual inspection can be performed by selecting those candidates thatappear to have domains present in SD+EODFR and/or low light tolerancepolypeptides, e.g., conserved functional domains.

Conserved regions can be identified by locating a region within theprimary amino acid sequence of an SD+EODFR and/or low light tolerancepolypeptide that is a repeated sequence, forms some secondary structure(e.g., helices and beta sheets), establishes positively or negativelycharged domains, or represents a protein motif or domain. See, e.g., thePfam web site describing consensus sequences for a variety of proteinmotifs and domains on the World Wide Web atsanger.ac.uk/Software/Pfam/and pfam.janelia.org/. A description of theinformation included at the Pfam database is described in Sonnhammer etal., Nucl. Acids Res., 26:320-322 (1998); Sonnhammer et al., Proteins,28:405-420 (1997); and Bateman et al., Nucl. Acids Res., 27:260-262(1999). Conserved regions also can be determined by aligning sequencesof the same or related polypeptides from closely related species.Closely related species preferably are from the same family. In someembodiments, alignment of sequences from two different species isadequate.

Typically, polypeptides that exhibit at least about 40% amino acidsequence identity are useful to identify conserved regions. Conservedregions of related polypeptides exhibit at least 45% amino acid sequenceidentity (e.g., at least 50%, at least 60%, at least 70%, at least 80%,or at least 90% amino acid sequence identity). In some embodiments, aconserved region exhibits at least 92%, 94%, 96%, 98%, or 99% amino acidsequence identity.

Amino acid sequences of functional homologs of the polypeptide set forthin SEQ ID NO:3 are provided in FIG. 1. Such functional homologs includeCeres CLONE ID no. 1844057 (SEQ ID NO:7), Ceres ANNOT ID no. 1469148(SEQ ID NO:22), Public GI ID no. 18390998 (SEQ ID NO:25), Ceres CLONE IDno. 1065656 (SEQ ID NO:32), Ceres CLONE ID no. 1652677 (SEQ ID NO:36),Public GI ID no. 92874556 (SEQ ID NO:49), Ceres CLONE ID no. 1329161(SEQ ID NO:53), Ceres CLONE ID no. 1030378 (SEQ ID NO:55), Ceres CLONEID no. 1413787 (SEQ ID NO:57), and Public GI ID no. 125543598 (SEQ IDNO:60). Other functional homologs of SEQ ID NO:3 include Ceres CLONE IDno. 1793691 (SEQ ID NO:5), Ceres CLONE ID no. 1933784 (SEQ ID NO:9),Ceres CLONE ID no. 100030408 (SEQ ID NO:10), Ceres CLONE ID no. 1837059(SEQ ID NO:12), Ceres CLONE ID no. 1793801 (SEQ ID NO:14), Ceres CLONEID no. 1855480 (SEQ ID NO:16), Ceres CLONE ID no. 1915644 (SEQ IDNO:18), Ceres CLONE ID no. 1898104 (SEQ ID NO:20), Ceres ANNOT ID no.1464241 (SEQ ID NO:24), Public GI ID no. 18697627 (SEQ ID NO:26), CeresCLONE ID no. 9391 (SEQ ID NO:28), Ceres CLONE ID no. 111154 (SEQ IDNO:30), Ceres CLONE ID no. 973975 (SEQ ID NO:34), Ceres CLONE ID no.676695 (SEQ ID NO:38), Ceres CLONE ID no. 680331 (SEQ ID NO:40), CeresCLONE ID no. 654515 (SEQ ID NO:42), Ceres CLONE ID no. 626154 (SEQ IDNO:44), Ceres CLONE ID no. 710603 (SEQ ID NO:46), Ceres CLONE ID no.648076 (SEQ ID NO:48), Ceres CLONE ID no. 749439 (SEQ ID NO:51), CeresCLONE ID no. 295936 (SEQ ID NO:59), Public GI ID no. 125525139 (SEQ IDNO:61), Public GI ID no. 115452643 (SEQ ID NO:62), Public GI ID no.24059889 (SEQ ID NO:63), Ceres ANNOT ID no. 6012747 (SEQ ID NO:65),Ceres ANNOT ID no. 6027628 (SEQ ID NO:67), and sequences identified asfunctional homologs of the sequences of FIG. 1, as set forth in thesequence listing. In some cases, a functional homolog of SEQ ID NO:3 hasan amino acid sequence with at least 40% sequence identity, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ ID NO:3.

Amino acid sequences of functional homologs of the polypeptide set forthin SEQ ID NO:70 are provided in FIG. 2. Such functional homologs includeCeres CLONE ID no. 1975934 (SEQ ID NO:72), Ceres ANNOT ID no. 1529913(SEQ ID NO:80), Ceres CLONE ID no. 977794 (SEQ ID NO:93), Public GI IDno. 42362378 (SEQ ID NO:96), Public GI ID no. 23899378 (SEQ ID NO:99),Public GI ID no. 15963346 (SEQ ID NO:101), Public GI ID no.15963344+B816 (SEQ ID NO:102), Public GI ID no. 92429657 (SEQ IDNO:103), Ceres CLONE ID no. 746644 (SEQ ID NO:105), Ceres CLONE ID no.623089 (SEQ ID NO:109), Ceres CLONE ID no. 1913678 (SEQ ID NO: 115), andPublic GI ID no. 115450609 (SEQ ID NO: 119). Other functional homologsof SEQ ID NO:70 include Ceres CLONE ID no. 1835084 (SEQ ID NO:74), CeresCLONE ID no. 1846153 (SEQ ID NO:76), Ceres CLONE ID no. 1930884 (SEQ IDNO:78), Ceres ANNOT ID no. 1493858 (SEQ ID NO:82), Ceres ANNOT ID no.1498646 (SEQ ID NO:84), Ceres ANNOT ID no. 1440974 (SEQ ID NO:86), CeresCLONE ID no. 1189183 (SEQ ID NO:88), Public GI ID no. 26450253 (SEQ IDNO:89), Public GI ID no. 15239719 (SEQ ID NO:90), Public GI ID no.15230194 (SEQ ID NO:91), Ceres CLONE ID no. 630905 (SEQ ID NO:95),Public GI ID no. 42362389 (SEQ ID NO:97), Public GI ID no. 70906129 (SEQID NO:98), Public GI ID no. 23899381 (SEQ ID NO:100), Ceres CLONE ID no.298166 (SEQ ID NO:107), Ceres CLONE ID no. 1448390 (SEQ ID NO:111),Ceres CLONE ID no. 1734216 (SEQ ID NO:113), Public GI LD no. 125542322(SEQ ID NO:116), Public GI ID no. 125532331 (SEQ ID NO:117), Public GIID no. 125541233 (SEQ ID NO:118), Public GI ID no. 125584844 (SEQ IDNO:120), Public GI ID no. 115482472 (SEQ ID NO:121), Public GI ID no.125575112 (SEQ ID NO:122), Ceres ANNOT ID no. 6003994 (SEQ ID NO:124),Ceres ANNOT ID no. 6068427 (SEQ ID NO:126), and sequences identified asfunctional homologs of the sequences of FIG. 2, as set forth in thesequence listing. In some cases, a functional homolog of SEQ ID NO:70has an amino acid sequence with at least 40% sequence identity, e.g.,50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or99% sequence identity, to the amino acid sequence set forth in SEQ IDNO:70.

Amino acid sequences of functional homologs of the polypeptide set forthin SEQ ID NO:129 are provided in FIG. 3. Such functional homologsinclude Public GI ID no. 34550779 (SEQ ID NO:133), Ceres CLONE ID no.1932235 (SEQ ID NO:137), Ceres CLONE ID no. 981738 (SEQ ID NO:201),Ceres CLONE ID no. 565974 (SEQ ID NO:209), Public GI ID no. 1352058 (SEQID NO:231), Public GI ID no. 11131101 (SEQ ID NO:234), Public GI ID no.4887018 (SEQ ID NO:236), Public GI ID no. 4887018 (SEQ ID NO:236), CeresCLONE ID no. 644455 (SEQ ID NO:247). Ceres CLONE ID no. 1731500 (SEQ IDNO:270), Public GI ID no. 20269063 (SEQ ID NO:300), Public GI ID no.50404477 (SEQ ID NO:302), and Public GI ID no. 62125392 (SEQ ID NO:303).Other functional homologs of SEQ ID NO:129 include Public GI ID no.32396293 (SEQ ID NO:130), Public GI ID no. 32396299 (SEQ ID NO:131),Public GI ID no. 32396295 (SEQ ID NO:132), Ceres CLONE ID no. 1855369(SEQ ID NO:135), Ceres CLONE ID no. 1948456 (SEQ ID NO:139). Ceres CLONEID no. 1920182 (SEQ ID NO:141), Ceres CLONE ID no. 1835797 (SEQ IDNO:143), Ceres CLONE ID no. 1794204 (SEQ ID NO:145), Ceres CLONE ID no.1853542 (SEQ ID NO:147), Ceres CLONE ID no. 1838776 (SEQ ID NO:149),Ceres CLONE ID no. 1854675 (SEQ ID NO:151), Ceres CLONE ID no. 1833078(SEQ ID NO:153), Ceres CLONE ID no. 1850667 (SEQ ID NO:155), Ceres CLONEID no. 1918745 (SEQ ID NO:157), Ceres CLONE ID no. 1929487 (SEQ IDNO:159), Ceres ANNOT ID no. 1497918 (SEQ ID NO:161). Ceres ANNOT ID no.1459563 (SEQ ID NO:163), Ceres ANNOT ID no. 1452610 (SEQ ID NO:165),Ceres ANNOT ID no. 1496539 (SEQ ID NO:167), Ceres ANNOT ID no. 1498819(SEQ ID NO:169). Ceres ANNOT ID no. 1446583 (SEQ ID NO:171), Ceres ANNOTID no. 1535123 (SEQ ID NO:173), Ceres ANNOT ID no. 1463397 (SEQ IDNO:175), Ceres ANNOT ID no. 1499563 (SEQ ID NO:177), Ceres ANNOT ID no.1495753 (SEQ ID NO:179), Ceres ANNOT ID no. 1488767 (SEQ ID NO:181).Ceres ANNOT ID no. 1522920 (SEQ ID NO:185), Ceres ANNOT ID no. 1469532(SEQ ID NO:187), Public GI ID no. 15219692 (SEQ ID NO:188), Public GI IDno. 18420964 (SEQ ID NO:189). Ceres CLONE ID no. 1342080 (SEQ IDNO:191), Ceres CLONE ID no. 123105 (SEQ ID NO:193), Ceres CLONE ID no.32727 (SEQ ID NO:195). Ceres CLONE ID no. 41161 (SEQ ID NO:197), CeresCLONE ID no. 37274 (SEQ ID NO:199), Ceres CLONE ID no. 538020 (SEQ IDNO:203), Ceres CLONE ID no. 476244 (SEQ ID NO:205), Ceres CLONE ID no.1623662 (SEQ ID NO:207), Ceres CLONE ID no. 626817 (SEQ ID NO:211),Ceres CLONE ID no. 537469 (SEQ ID NO:213), Ceres CLONE ID no. 582463(SEQ ID NO:215), Ceres CLONE ID no. 1069818 (SEQ ID NO:217), Ceres CLONEID no. 511737 (SEQ ID NO:219), Ceres CLONE ID no. 565422 (SEQ IDNO:221), Ceres CLONE ID no. 514595 (SEQ ID NO:223), Ceres CLONE ID no.566396 (SEQ ID NO:225), Ceres CLONE ID no. 612705 (SEQ ID NO:227), CeresCLONE ID no. 564134 (SEQ ID NO:229), Public GI ID no. 92872146 (SEQ IDNO:230), Public GI ID no. 11131103 (SEQ TD NO:232), Public GI ID no.416641 (SEQ ID NO:233), Public GI ID no. 11131105 (SEQ ID NO:235),Public GI ID no. 4887016 (SEQ ID NO:237), Public GI ID no. 4887022 (SEQID NO:238), Public GI ID no. 81074526 (SEQ ID NO:239), Ceres CLONE IDno. 742023 (SEQ ID NO:241), Ceres CLONE ID no. 576268 (SEQ ID NO:243),Ceres CLONE ID no. 615386 (SEQ ID NO:245), Ceres CLONE ID no. 756966(SEQ ID NO:249), Ceres CLONE ID no. 1052710 (SEQ ID NO:251), Ceres CLONEID no. 697018 (SEQ ID NO:253), Ceres CLONE ID no. 618577 (SEQ IDNO:255), Ceres CLONE ID no. 935194 (SEQ ID NO:257), Ceres CLONE ID no.1557429 (SEQ ID NO:259), Ceres CLONE ID no. 305337 (SEQ ID NO:261),Ceres CLONE ID no. 100872943 (SEQ ID NO:262), Ceres CLONE ID no. 305454(SEQ ID NO:264), Ceres CLONE ID no. 1534670 (SEQ ID NO:266), Ceres CLONEID no. 207963 (SEQ ID NO:268), Public GI ID no. 20257219 (SEQ IDNO:271), Ceres CLONE ID no. 1876818 (SEQ ID NO:273), Ceres CLONE ID no.1817533 (SEQ ID NO:275), Ceres CLONE ID no. 1958631 (SEQ ID NO:277),Ceres CLONE ID no. 1963215 (SEQ ID NO:279), Ceres CLONE ID no. 1770022(SEQ ID NO:281), Ceres CLONE ID no. 1796223 (SEQ ID NO:283), Ceres CLONEID no. 2016695 (SEQ ID NO:285), Ceres CLONE ID no. 1757085 (SEQ IDNO:287), Ceres CLONE ID no. 1769256 (SEQ ID NO:289), Ceres CLONE ID no.1994871 (SEQ ID NO:291), Public GI ID no. 17154533 (SEQ ID NO:292),Public GI ID no. 125557426 (SEQ ID NO:293), Public GI ID no. 125524736(SEQ ID NO:294), Public GI ID no. 125527656 (SEQ ID NO:295), Public GIID no. 125599342 (SEQ ID NO:296), Public GI ID no. 125569626 (SEQ IDNO:297), Public GI ID no. 115465401 (SEQ ID NO:298), Public GI ID no.40539038 (SEQ ID NO:299), Public GI ID no. 20269059 (SEQ ID NO:301),Public GI ID no. 110826446 (SEQ ID NO:304), Ceres ANNOT ID no. 6029073(SEQ ID NO:306), Ceres ANNOT ID no. 6011329 (SEQ ID NO:308), Ceres ANNOTID no. 6034498 (SEQ ID NO:310). Ceres ANNOT ID no. 6095057 (SEQ IDNO:312), Ceres ANNOT ID no. 6095058 (SEQ ID NO:314), and sequencesidentified as functional homologs of the sequences of FIG. 3, as setforth in the sequence listing. In some cases, a functional homolog ofSEQ ID NO:129 has an amino acid sequence with at least 40% sequenceidentity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%,95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence setforth in SEQ ID NO:129.

Amino acid sequences of functional homologs of the polypeptide set forthin SEQ ID NO:317 are provided in FIG. 4. Such functional homologsinclude Ceres CLONE ID no. 1842125 (SEQ ID NO:319), Ceres ANNOT ID no.1461360 (SEQ ID NO:321). Ceres CLONE ID no. 480906 (SEQ ID NO:327),Public GI ID no. 92889352 (SEQ ID NO:330), and Public GI ID no. 56201850(SEQ ID NO:330). Other functional homologs of SEQ ID NO:317 includeCeres ANNOT ID no. 1440334 (SEQ ID NO:323), Ceres ANNOT ID no. 1493205(SEQ ID NO:325), Ceres CLONE ID no. 482270 (SEQ ID NO:329), Public GI IDno. 125571531 (SEQ ID NO:332), Ceres ANNOT ID no. 6042411 (SEQ IDNO:334), and sequences identified as functional homologs of thesequences of FIG. 4, as set forth in the sequence listing. In somecases, a functional homolog of SEQ ID NO:317 has an amino acid sequencewith at least 40% sequence identity, e.g., 50%, 52%, 56%, 59%, 61%, 65%,70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to theamino acid sequence set forth in SEQ ID NO:317.

Amino acid sequences of functional homologs of the polypeptide set forthin SEQ ID NO:337 are provided in FIG. 5. Such functional homologsinclude Ceres CLONE ID no. 952050 (SEQ ID NO:339), Public GI ID no.115477050 (SEQ ID NO:349), Public GI ID no. 87162911 (SEQ ID NO:355),Ceres CLONE ID no. 1790901 (SEQ ID NO:357), Ceres CLONE ID no. 1460088(SEQ ID NO:370), Ceres CLONE ID no. 1734065 (SEQ ID NO:393), Ceres CLONEID no. 473509 (SEQ TD NO:395), Ceres CLONE ID no. 849918 (SEQ IDNO:401), Ceres CLONE ID no. 633470 (SEQ ID NO:409), Ceres CLONE ID no.1808334 (SEQ ID NO:417), and Ceres ANNOT ID no. 1525600 (SEQ ID NO:437).Other functional homologs of SEQ ID NO:337 include Ceres CLONE ID no.1265097 (SEQ ID NO:341), Ceres CLONE ID no. 942980 (SEQ ID NO:343),Public GI ID no. 37901055 (SEQ ID NO:344), Ceres CLONE ID no. 1609912(SEQ ID NO:346), Public GI ID no. 76446335 (SEQ ID NO:347), Public GI IDno. 125560204 (SEQ ID NO:348), Public GI ID no. 125303087 (SEQ IDNO:350), Public GI ID no. 115460088 (SEQ ID NO:351), Public GI ID no.125591385 (SEQ ID NO:352), Public GI ID no. 115447931 (SEQ ID NO:353),Public GI ID no. 92893514 (SEQ ID NO:354), Ceres CLONE ID no. 2019320(SEQ ID NO:359), Ceres CLONE ID no. 1890013 (SEQ ID NO:361), Public GIID no. 20340241 (SEQ ID NO:362), Ceres CLONE ID no. 25801 (SEQ IDNO:364), Public GI ID no. 9743343 (SEQ ID NO:365), Public GI ID no.15238072 (SEQ ID NO:366), Public GI ID no. 15222553 (SEQ ID NO:367),Public GI ID no. 21554155 (SEQ ID NO:368). Ceres CLONE ID no. 374439(SEQ ID NO:372), Ceres CLONE ID no. 1465572 (SEQ ID NO:374), Ceres CLONEID no. 1565524 (SEQ ID NO:376), Ceres CLONE ID no. 322302 (SEQ IDNO:378), Ceres CLONE ID no. 101136485 (SEQ ID NO:379), Ceres CLONE IDno. 1376133 (SEQ ID NO:381), Ceres CLONE ID no. 1374381 (SEQ ID NO:383),Ceres CLONE ID no. 1566473 (SEQ ID NO:385), Ceres CLONE ID no. 318088(SEQ ID NO:387), Ceres CLONE ID no. 1452604 (SEQ ID NO:389), Ceres CLONEID no. 337906 (SEQ ID NO:391), Ceres CLONE ID no. 1662513 (SEQ IDNO:397). Ceres CLONE ID no. 1662527 (SEQ ID NO:399), Ceres CLONE ID no.571184 (SEQ ID NO:403), Ceres CLONE ID no. 665689 (SEQ ID NO:405), CeresCLONE ID no. 1365853 (SEQ ID NO:407). Ceres CLONE ID no. 1052457 (SEQ IDNO:411), Ceres CLONE ID no. 579918 (SEQ ID NO:413), Ceres CLONE ID no.863299 (SEQ ID NO:415), Ceres CLONE ID no. 1855611 (SEQ ID NO:419),Ceres CLONE ID no. 1845975 (SEQ TD NO:421), Ceres CLONE ID no. 1808298(SEQ ID NO:423), Ceres CLONE ID no. 1841236 (SEQ ID NO:425), Ceres CLONEID no. 1808269 (SEQ ID NO:427), Ceres CLONE ID no. 1850628 (SEQ IDNO:429), Ceres CLONE ID no. 1846911 (SEQ ID NO:431), Ceres CLONE ID no.1916014 (SEQ ID NO:433), Ceres CLONE ID no. 1842594 (SEQ ID NO:435),Ceres ANNOT ID no. 1472192 (SEQ ID NO:439), Ceres ANNOT ID no. 1447489(SEQ ID NO:441), Ceres ANNOT ID no. 1513000 (SEQ ID NO:443), Ceres ANNOTID no. 1438658 (SEQ ID NO:445), Ceres ANNOT ID no. 1497255 (SEQ IDNO:447), Ceres ANNOT ID no. 6092104 (SEQ ID NO:449), Ceres ANNOT ID no.6041700 (SEQ ID NO:451), Ceres ANNOT ID no. 6007297 (SEQ ID NO:453), andsequences identified as functional homologs of the sequences of FIG. 5,as set forth in the sequence listing. In some cases, a functionalhomolog of SEQ TD NO:337 has an amino acid sequence with at least 40%sequence identity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%,85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acidsequence set forth in SEQ ID NO:337.

Amino acid sequences of functional homologs of the polypeptide set forthin SEQ ID NO:456 are provided in FIG. 6. Such functional homologsinclude Public GI ID no. 58430585 (SEQ ID NO:457), Ceres CLONE ID no.1842825 (SEQ TD NO:466). Ceres ANNOT ID no. 1449721 (SEQ ID NO:474),Public GI ID no. 41323978 (SEQ ID NO:475), Public GI ID no. 2895186 (SEQID NO:478), Public GI ID no. 22854950 (SEQ ID NO:481), Public GI ID no.116010474 (SEQ ID NO:485), Public GI ID no. 4091804 (SEQ ID NO:488),Public GI ID no. 60459257 (SEQ ID NO:494), Public GI ID no. 45544881(SEQ ID NO:496), Public GI ID no. 36789802 (SEQ ID NO:498), Public GI LDno. 92875402 (SEQ ID NO:508), Public GI ID no. 118406898 (SEQ IDNO:510), Public GI ID no. 107770485 (SEQ ID NO:511), Public GI ID no.21655154 (SEQ ID NO:532), Public GI ID no. 90657642 (SEQ ID NO:536), andCeres CLONE ID no. 1569555 (SEQ ID NO:1842). Other homologs of SEQ IDNO:456 include Public GI ID no. 66841018 (SEQ ID NO:458), Public GI IDno. 66841020 (SEQ ID NO:459), Public GI ID no. 108859343 (SEQ IDNO:460), Ceres CLONE ID no. 1937613 (SEQ ID NO:462), Ceres CLONE ID no.1834027 (SEQ ID NO:464), Ceres ANNOT ID no. 1477832 (SEQ ID NO:468),Ceres ANNOT ID no. 1482536 (SEQ ID NO:470), Ceres ANNOT ID no. 1478227(SEQ ID NO:472). Ceres CLONE ID no. 19906 (SEQ ID NO:478), Public GI IDno. 2895184 (SEQ ID NO:479), Public GI ID no. 2895188 (SEQ ID NO:480),Public GI ID no. 11037313 (SEQ ID NO:482), Public GI ID no. 22854908(SEQ ID NO:483), Public GI ID no. 40787165 (SEQ ID NO:484), Public GI IDno. 116010475 (SEQ ID NO:486), Public GI ID no. 3341723 (SEQ ID NO:487),Public GI ID no. 4091806 (SEQ ID NO:489), Ceres CLONE ID no. 523203 (SEQID NO:491), Ceres CLONE ID no. 463157 (SEQ ID NO:493), Public GI ID no.61611678 (SEQ ID NO:495), Public GI ID no. 45544887 (SEQ ID NO:497),Public GI ID no. 36789793 (SEQ ID NO:481). Ceres CLONE ID no. 907473(SEQ ID NO:501), Ceres CLONE ID no. 1674443 (SEQ ID NO:503), Ceres CLONEID no. 1559496 (SEQ ID NO:505), Ceres CLONE ID no. 530984 (SEQ IDNO:507), Public GI ID no. 61611682 (SEQ ID NO:509), Public GI LD no.36789785 (SEQ ID NO:512), Ceres CLONE ID no. 702632 (SEQ ID NO:514),Public GI ID no. 61657299 (SEQ ID NO:515), Public GI ID no. 10946337(SEQ ID NO:516), Ceres CLONE ID no. 1996408 (SEQ ID NO:518). Ceres CLONEID no. 1725313 (SEQ ID NO:520), Public GI ID no. 78058606 (SEQ IDNO:521), Public GI ID no. 125538317 (SEQ ID NO:522), Public GI ID no.125556324 (SEQ ID NO:523), Public GI ID no. 125548890 (SEQ ID NO:524),Public GI ID no. 93211100 (SEQ ID NO:525), Public GI ID no. 115444217(SEQ ID NO:526), Public GI ID no. 115467558 (SEQ ID NO:527), Public GIID no. 11094209 (SEQ ID NO:528), Public GI ID no. 125596830 (SEQ LDNO:529), Public GI ID no. 115469296 (SEQ ID NO:530), Public GI ID no.115447239 (SEQ ID NO:531), Public GI ID no. 21667485 (SEQ ID NO:533),Public GI ID no. 21667475 (SEQ ID NO:534), Public GI ID no. 21655158(SEQ ID NO:535), and sequences identified as functional homologs of thesequences of FIG. 6, as set forth in the sequence listing. In somecases, a functional homolog of SEQ ID NO:456 has an amino acid sequencewith at least 40% sequence identity, e.g., 50%, 52%, 56%, 59%, 61%, 65%,70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to theamino acid sequence set forth in SEQ ID NO:456.

Amino acid sequences of functional homologs of the polypeptide set forthin SEQ ID NO:634 are provided in FIG. 7. Such functional homologsinclude Public GI ID no. 98961985 (SEQ ID NO:637). Other functionalhomologs of SEQ ID NO:634 include Ceres CLONE ID no. 1916112 (SEQ IDNO:636), Public GI ID no. 9369405 (SEQ ID NO:638), Public GI ID no.9369406 (SEQ ID NO:639), Ceres CLONE ID no. 1238706 (SEQ ID NO:641), andsequences identified as functional homologs of the sequences of FIG. 7,as set forth in the sequence listing. In some cases, a functionalhomolog of SEQ ID NO:634 has an amino acid sequence with at least 40%sequence identity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%,85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acidsequence set forth in SEQ ID NO:634.

Amino acid sequences of functional homologs of the polypeptide set forthin SEQ ID NO:644 are provided in FIG. 8. Such functional homologsinclude SEQ ID NO:645, Ceres CLONE ID no. 1849479 (SEQ ID NO:767),Public GI ID no. 89275008 (SEQ ID NO:796), Public GI ID no. 120400525(SEQ ID NO:797), Public GI ID no. 98980426 (SEQ ID NO:804), Public GI IDno. 71983373 (SEQ ID NO:808), Public GI ID no. 41351817 (SEQ ID NO:809),Public GI ID no. 76446191 (SEQ ID NO:811), Public GI ID no. 5616086 (SEQID NO:813). Ceres CLONE ID no. 1052602 (SEQ ID NO:826), Public GI ID no.72068957 (SEQ ID NO:830), Public GI ID no. 71534113 (SEQ ID NO:831),Public GI ID no. 37147896 (SEQ ID NO:832), Public GI ID no. 92918850(SEQ ID NO:834), Public GI ID no. 40647095 (SEQ ID NO:835), Ceres ANNOTID no. 1527711 (SEQ ID NO:837), Public GI ID no. 71041116 (SEQ IDNO:838), Public GI ID no. 12003384 (SEQ ID NO:839), Public GI ID no.18535580 (SEQ ID NO:840), and Public GI ID no. 115353971 (SEQ IDNO:1843). Other functional homologs of SEQ ID NO:644 include Ceres CLONEID no. 991178 (SEQ ID NO:647), Ceres CLONE ID no. 1626038 (SEQ IDNO:649), Ceres CLONE ID no. 341615 (SEQ ID NO:651), Ceres CLONE ID no.1832518 (SEQ ID NO:653), Ceres CLONE ID no. 1832588 (SEQ ID NO:655),Ceres CLONE ID no. 1936806 (SEQ ID NO:657), Ceres CLONE ID no. 973892(SEQ ID NO:659), Ceres CLONE ID no. 565251 (SEQ ID NO:661), Ceres CLONEID no. 681088 (SEQ ID NO:663), Ceres CLONE ID no. 707775 (SEQ IDNO:665), Ceres CLONE ID no. 453357 (SEQ ID NO:667), Ceres CLONE ID no.1916958 (SEQ ID NO:669), Ceres CLONE ID no. 1940632 (SEQ ID NO:671),Ceres CLONE ID no. 476784 (SEQ ID NO:673). Ceres CLONE ID no. 1869284(SEQ ID NO:675), Public GI ID no. 125540662 (SEQ ID NO:676), Ceres CLONEID no. 1648272 (SEQ ID NO:678), Ceres CLONE ID no. 1987804 (SEQ IDNO:680), Ceres CLONE ID no. 1675695 (SEQ ID NO:682), Ceres CLONE ID no.1169111 (SEQ ID NO:684), Ceres CLONE ID no. 572121 (SEQ ID NO:686),Ceres CLONE ID no. 1674836 (SEQ ID NO:688), Ceres ANNOT ID no. 1486207(SEQ ID NO:690), Ceres CLONE ID no. 2023610 (SEQ ID NO:692), Ceres ANNOTID no. 1496976 (SEQ ID NO:694), Public GI ID no. 116310031 (SEQ IDNO:695), Ceres CLONE ID no. 1626363 (SEQ ID NO:697), Ceres ANNOT ID no.1483747 (SEQ ID NO:699), Ceres ANNOT ID no. 1471330 (SEQ ID NO:701),Ceres CLONE ID no. 101144964 (SEQ ID NO:702), Ceres ANNOT ID no. 1439439(SEQ ID NO:704), Ceres CLONE ID no. 1446565 (SEQ ID NO:706), Ceres CLONEID no. 1951962 (SEQ ID NO:708). Ceres CLONE ID no. 100960656 (SEQ IDNO:709), Ceres CLONE ID no. 285154 (SEQ ID NO:711), Public GI ID no.61968916 (SEQ ID NO:712), Public GI ID no. 118026854 (SEQ ID NO:713),Public GI ID no. 63098612 (SEQ ID NO:714), Ceres ANNOT ID no. 1522310(SEQ ID NO:716), Ceres CLONE ID no. 1854375 (SEQ ID NO:718), Ceres CLONEID no. 709819 (SEQ ID NO:720), Public GI ID no. 115447695 (SEQ IDNO:721), Ceres CLONE ID no. 1726356 (SEQ ID NO:723), Ceres CLONE ID no.1762419 (SEQ ID NO:725), Public GI ID no. 63098606 (SEQ ID NO:726),Ceres CLONE ID no. 1766572 (SEQ ID NO:728), Ceres CLONE ID no. 281871(SEQ ID NO:730), Ceres CLONE ID no. 1560970 (SEQ ID NO:732), Ceres CLONEID no. 1760747 (SEQ ID NO:734), Ceres ANNOT ID no. 1438772 (SEQ IDNO:736), Ceres ANNOT ID no. 1447378 (SEQ ID NO:738), Ceres ANNOT ID no.1453360 (SEQ ID NO:740), Public GI ID no. 33637698 (SEQ ID NO:741),Public GI ID no. 118026860 (SEQ ID NO:742), Public GI ID no. 60116232(SEQ ID NO:743), Public GI ID no. 115477639 (SEQ ID NO:744), Public GIID no. 126567023 (SEQ ID NO:745), Ceres CLONE ID no. 988971 (SEQ IDNO:747), Ceres CLONE ID no. 1464521 (SEQ ID NO:749), Public GI ID no.63098610 (SEQ ID NO:750), Public GI ID no. 126566972 (SEQ ID NO:751),Ceres CLONE ID no. 1556129 (SEQ ID NO:753), Ceres CLONE ID no. 1761385(SEQ ID NO:755), Ceres ANNOT ID no. 1488325 (SEQ ID NO:757), Ceres ANNOTID no. 1460483 (SEQ ID NO:759), Ceres CLONE ID no. 1837825 (SEQ IDNO:761), Public GI ID no. 27228310 (SEQ ID NO:762), Public GI ID no.117653881 (SEQ ID NO:763), Public GI ID no. 115480233 (SEQ ID NO:764),Public GI ID no. 37694048 (SEQ ID NO:765), Ceres CLONE ID no. 1934653(SEQ ID NO:769), Ceres CLONE ID no. 1608106 (SEQ ID NO:771), Ceres CLONEID no. 1604576 (SEQ ID NO:773), Public GI ID no. 55824656 (SEQ IDNO:774), Ceres CLONE ID no. 1620272 (SEQ ID NO:776), Ceres CLONE ID no.1853170 (SEQ ID NO:778), Public GI ID no. 79013962 (SEQ ID NO:779),Public GI ID no. 98975385 (SEQ ID NO:780), Ceres ANNOT ID no. 1438775(SEQ ID NO:782), Public GI ID no. 23495460 (SEQ ID NO:783), Public GI IDno. 98975377 (SEQ ID NO:784), Ceres ANNOT ID no. 1438776 (SEQ IDNO:786), Ceres CLONE ID no. 1853601 (SEQ ID NO:788), Ceres CLONE ID no.1609048 (SEQ ID NO:790), Ceres CLONE ID no. 322305 (SEQ ID NO:792),Ceres CLONE ID no. 1823713 (SEQ ID NO:794), Public GI ID no. 3660548(SEQ ID NO:795), Public GI ID no. 56154991 (SEQ ID NO:798), Public GI IDno. 2980802 (SEQ ID NO:799), Public GI ID no. 7269398 (SEQ ID NO:800),Public GI ID no. 18416557 (SEQ ID NO:801), Public GI ID no. 56154992(SEQ ID NO:802), Public GI ID no. 4091984 (SEQ ID NO:803), Public GI IDno. 1899058 (SEQ ID NO:805), Public GI ID no. 56154990 (SEQ ID NO:806),Public GI ID no. 18416562 (SEQ ID NO:807), Public GI ID no. 38683266(SEQ ID NO:810), Public GI ID no. 39983638 (SEQ ID NO:812), Public GI IDno. 38426954 (SEQ ID NO:814), Public GI ID no. 38426948 (SEQ ID NO:815),Public GI ID no. 38146944 (SEQ ID NO:816), Public GI ID no. 38426952(SEQ ID NO:817), Public GI ID no. 20303011 (SEQ ID NO:818), Public GI IDno. 66269982 (SEQ ID NO:819), Public GI ID no. 89212816 (SEQ ID NO:820),Public GI ID no. 20303015 (SEQ ID NO:821), Public GI ID no. 38426950(SEQ ID NO:822), Public GI ID no. 15242244 (SEQ ID NO:823), Public GI IDno. 116831599 (SEQ ID NO:824), Public GI ID no. 66269671 (SEQ IDNO:827), Ceres ANNOT ID no. 1468919 (SEQ ID NO:829), Public GI ID no.57903606 (SEQ ID NO:833), Public GI ID no. 45826358 (SEQ ID NO:841),Ceres ANNOT ID no. 6085912 (SEQ ID NO:843), Ceres ANNOT ID no. 6026171(SEQ ID NO:845), Ceres ANNOT ID no. 6031706 (SEQ ID NO:847), andsequences listing identified as functional homologs of the sequences ofFIG. 8, as set forth in the sequence. In some cases, a functionalhomolog of SEQ ID NO:644 has an amino acid sequence with at least 40%sequence identity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%,85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acidsequence set forth in SEQ ID NO:644.

Amino acid sequences of functional homologs of the polypeptide set forthin SEQ ID NO:850 are provided in FIG. 9. Such functional homologsinclude Ceres CLONE ID no. 1833093 (SEQ ID NO:853), Ceres ANNOT ID no.1502190 (SEQ ID NO:857), Ceres CLONE ID no. 565641 (SEQ ID NO:876),Public GI ID no. 87240507 (SEQ ID NO:877), Ceres CLONE ID no. 1325382(SEQ ID NO:881), Ceres CLONE ID no. 1558265 (SEQ ID NO:885), Ceres CLONEID no. 1823669 (SEQ ID NO:895), and Public GI ID no. 115464921 (SEQ IDNO:898). Other functional homologs of SEQ ID NO:850 include Ceres CLONEID no. 100040598 (SEQ ID NO:851), Ceres CLONE ID no. 1847967 (SEQ IDNO:855), Ceres ANNOT ID no. 1449186 (SEQ ID NO:859), Ceres ANNOT ID no.1466723 (SEQ ID NO:861), Public GI ID no. 21805688 (SEQ ID NO:862),Public GI ID no. 9795609 (SEQ ID NO:863), Public GI ID no. 13877535 (SEQID NO:864), Public GI ID no. 15232547 (SEQ ID NO:865), Public GI ID no.15238851 (SEQ ID NO:866), Ceres CLONE ID no. 123863 (SEQ ID NO:868),Ceres CLONE ID no. 652496 (SEQ ID NO:870), Ceres CLONE ID no. 1656707(SEQ ID NO:872), Ceres CLONE ID no. 1660346 (SEQ ID NO:874), Ceres CLONEID no. 678878 (SEQ ID NO:879), Ceres CLONE ID no. 340102 (SEQ IDNO:883), Ceres CLONE ID no. 330491 (SEQ ID NO:887), Ceres CLONE ID no.992304 (SEQ ID NO:889), Ceres CLONE ID no. 1509925 (SEQ ID NO:891),Ceres CLONE ID no. 1543852 (SEQ ID NO:893), Ceres CLONE ID no. 1785736(SEQ ID NO:897), Ceres ANNOT ID no. 6079909 (SEQ ID NO:900), Ceres ANNOTID no. 6040353 (SEQ ID NO:902), Ceres ANNOT ID no. 6100173 (SEQ IDNO:904), and sequences listing identified as functional homologs of thesequences of FIG. 9, as set forth in the sequence. In some cases, afunctional homolog of SEQ ID NO:850 has an amino acid sequence with atleast 40% sequence identity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%,75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to theamino acid sequence set forth in SEQ ID NO:850.

Amino acid sequences of functional homologs of the polypeptide set forthin SEQ ID NO:907 are provided in FIG. 10. Such functional homologsinclude Ceres CLONE ID no. 1940797 (SEQ ID NO:909), Ceres ANNOT ID no.1538900 (SEQ ID NO:911). Ceres CLONE ID no. 1126868 (SEQ ID NO:922),Public GI ID no. 89257684 (SEQ ID NO:923), Public GI ID no. 124360460(SEQ ID NO:929), Public GI ID no. 62865694 (SEQ ID NO:931), Public GI IDno. 62865692 (SEQ ID NO:932), Ceres CLONE ID no. 260368 (SEQ ID NO:936),Ceres CLONE ID no. 1873510 (SEQ ID NO:947), Public GI ID no. 125541662(SEQ ID NO:948), Public GI ID no. 48716268 (SEQ ID NO:950), and PublicGI ID no. 62865696 (SEQ ID NO:1844). Other functional homologs of SEQ IDNO:907 include Ceres ANNOT ID no. 1529131 (SEQ ID NO:913), Ceres ANNOTID no. 1454060 (SEQ ID NO:915), Ceres ANNOT ID no. 1442787 (SEQ IDNO:917), Ceres ANNOT ID no. 1452648 (SEQ ID NO:919), Public GI ID no.2245140 (SEQ ID NO:920), Public GI ID no. 89274212 (SEQ ID NO:924),Ceres CLONE ID no. 1104523 (SEQ ID NO:926), Ceres CLONE ID no. 654265(SEQ ID NO:928), Public GI ID no. 42627704 (SEQ ID NO:930), Ceres CLONEID no. 887222 (SEQ ID NO:934), Public GI ID no. 62865690 (SEQ IDNO:937), Public GI ID no. 64175600 (SEQ ID NO:938), Public GI ID no.64175634 (SEQ ID NO:939), Public GI ID no. 64175606 (SEQ ID NO:940),Public GI ID no. 64175648 (SEQ ID NO:941), Ceres CLONE ID no. 312184(SEQ ID NO:943), Ceres CLONE ID no. 380740 (SEQ ID NO:945), Public GI IDno. 125531536 (SEQ ID NO:949), and sequences identified as functionalhomologs of the sequences of FIG. 10, as set forth in the sequencelisting. In some cases, a functional homolog of SEQ ID NO:907 has anamino acid sequence with at least 40% sequence identity, e.g., 50%, 52%,56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:907.

Amino acid sequences of functional homologs of the polypeptide set forthin SEQ ID NO:953 are provided in FIG. 11. Such functional homologsinclude Ceres CLONE ID no. 1798705 (SEQ ID NO:955), Ceres ANNOT ID no.1458907 (SEQ ID NO:963), Ceres CLONE ID no. 1090409 (SEQ ID NO:971),Ceres CLONE ID no. 479817 (SEQ ID NO:977), Ceres CLONE ID no. 1041793(SEQ ID NO:979), Ceres CLONE ID no. 684633 (SEQ ID NO:985), Ceres CLONEID no. 371815 (SEQ ID NO:991), Ceres CLONE ID no. 1686460 (SEQ IDNO:993), Ceres CLONE ID no. 1448595 (SEQ ID NO:995), Ceres CLONE ID no.1734477 (SEQ ID NO:999), Ceres CLONE ID no. 1605693 (SEQ ID NO:1005),Ceres CLONE ID no. 1757400 (SEQ ID NO:1009), and Public GI ID no.115434334 (SEQ ID NO:1015). Other functional homologs of SEQ ID NO:953include Ceres CLONE ID no. 1793754 (SEQ ID NO:957), Ceres CLONE ID no.1938045 (SEQ ID NO:959), Ceres CLONE ID no. 1850004 (SEQ ID NO:961),Ceres ANNOT ID no. 1489548 (SEQ ID NO:965), Public GI ID no. 22329538(SEQ ID NO:966), Public GI ID no. 18404714 (SEQ ID NO:967), Ceres CLONEID no. 1110032 (SEQ ID NO:969), Ceres CLONE ID no. 1095353 (SEQ IDNO:973), Ceres CLONE ID no. 872121 (SEQ ID NO:975), Ceres CLONE ID no.562208 (SEQ ID NO:981), Ceres CLONE ID no. 1042364 (SEQ ID NO:983),Ceres CLONE ID no. 1031873 (SEQ ID NO:987), Ceres CLONE ID no. 1377698(SEQ ID NO:989), Ceres CLONE ID no. 1742945 (SEQ ID NO:997), Ceres CLONEID no. 1742053 (SEQ ID NO:1001), Ceres CLONE ID no. 1728365 (SEQ IDNO:1003), Ceres CLONE ID no. 1609807 (SEQ ID NO:1007), Ceres CLONE IDno. 1778566 (SEQ ID NO:1011), Ceres CLONE ID no. 2020580 (SEQ IDNO:1013), Public GI ID no. 125524285 (SEQ ID NO:1014), Public GI ID no.125568898 (SEQ ID NO:1016). Ceres ANNOT ID no. 6055303 (SEQ ID NO:1018),and sequences identified as functional homologs of the sequences of FIG.11, as set forth in the sequence listing. In some cases, a functionalhomolog of SEQ ID NO:953 has an amino acid sequence with at least 40%sequence identity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%,85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acidsequence set forth in SEQ ID NO:953.

Amino acid sequences of functional homologs of the polypeptide set forthin SEQ ID NO:1024 are provided in FIG. 12. Such functional homologsinclude Ceres ANNOT ID no. 1452905 (SEQ ID NO:1029), Ceres CLONE ID no.956176 (SEQ ID NO:1039), Public GI ID no. 92870366 (SEQ ID NO:1040),Ceres CLONE ID no. 294166 (SEQ ID NO:1042), and Public GI ID no.125543067 (SEQ ID NO:1043). Other functional homologs of SEQ ID NO:1024include SEQ ID NO:1025, Ceres ANNOT ID no. 1442522 (SEQ ID NO:1027),Public GI ID no. 8778818 (SEQ ID NO:1030), Ceres CLONE ID no. 108095(SEQ ID NO:1032), Public GI ID no. 18394821 (SEQ ID NO:1033), CeresCLONE ID no. 6332 (SEQ ID NO:1035), Ceres CLONE ID no. 1069047 (SEQ IDNO:1037), Public GI ID no. 115480956 (SEQ ID NO:1044), and sequencesidentified as functional homologs of the sequences of FIG. 12, as setforth in the sequence listing. In some cases, a functional homolog ofSEQ ID NO:1024 has an amino acid sequence with at least 40% sequenceidentity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%,95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence setforth in SEQ ID NO:1024.

Amino acid sequences of functional homologs of the polypeptide set forthin SEQ ID NO:1047 are provided in FIG. 13. Such functional homologsinclude Ceres CLONE ID no. 1837694 (SEQ ID NO:1053), Ceres ANNOT ID no.1483367 (SEQ ID NO:1057), Ceres CLONE ID no. 1077781 (SEQ ID NO:1083),Ceres CLONE ID no. 471026 (SEQ ID NO:1085), Public GI ID no. 92888885(SEQ ID NO:1099), Public GI ID no. 45544873 (SEQ ID NO:1100), Public GIID no. 45758663 (SEQ ID NO:1101). Ceres CLONE ID no. 772927 (SEQ IDNO:1105), Ceres CLONE ID no. 895080 (SEQ ID NO:1111), Ceres CLONE ID no.1806128 (SEQ ID NO:1131), Public GI ID no. 115458192 (SEQ ID NO: 1134),and Public GI ID no. 82470795 (SEQ ID NO:1139). Other functionalhomologs of SEQ ID NO:1047 include Ceres CLONE ID no. 1837746 (SEQ IDNO:1049), Ceres CLONE ID no. 1834764 (SEQ ID NO:1051), Ceres CLONE IDno. 1853547 (SEQ ID NO:1055), Ceres ANNOT ID no. 1474088 (SEQ IDNO:1059), Ceres ANNOT ID no. 1536919 (SEQ ID NO:1061), Ceres ANNOT IDno. 1467033 (SEQ ID NO:1063), Ceres ANNOT ID no. 1485401 (SEQ IDNO:1065), Ceres ANNOT ID no. 1486505 (SEQ ID NO:1067), Public GI ID no.17065054 (SEQ ID NO:1068), Public GI ID no. 30694690 (SEQ ID NO:1069),Ceres CLONE ID no. 12997 (SEQ ID NO:1071), Public GI ID no. 30694694(SEQ ID NO:1072), Public GI ID no. 42572167 (SEQ ID NO:1073), Public GIID no. 110739742 (SEQ ID NO:1074). Public GI ID no. 18412263 (SEQ IDNO:1075), Ceres CLONE ID no. 36412 (SEQ ID NO:1077), Public GI ID no.18399792 (SEQ ID NO:1078), Ceres CLONE ID no. 924 (SEQ ID NO:1080),Public GI ID no. 15238000 (SEQ ID NO:1081), Ceres CLONE ID no. 1626330(SEQ ID NO:1087), Ceres CLONE ID no. 1650419 (SEQ ID NO:1089), CeresCLONE ID no. 1641329 (SEQ ID NO:1091), Ceres CLONE ID no. 1620406 (SEQID NO:1093), Ceres CLONE ID no. 546832 (SEQ ID NO:1095), Ceres CLONE IDno. 1243138 (SEQ ID NO:1097), Public GI ID no. 92887260 (SEQ IDNO:1098), Ceres CLONE ID no. 885628 (SEQ ID NO: 1103), Ceres CLONE IDno. 1376391 (SEQ ID NO: 1107), Ceres CLONE ID no. 465893 (SEQ ID NO:1109), Ceres CLONE ID no. 218243 (SEQ ID NO:1113), Ceres CLONE ID no.1558456 (SEQ ID NO: 1115), Ceres CLONE ID no. 343008 (SEQ ID NO:1117),Ceres CLONE ID no. 218463 (SEQ ID NO:1119), Ceres CLONE ID no. 1565409(SEQ ID NO:1121), Ceres CLONE ID no. 1060968 (SEQ ID NO: 1123), CeresCLONE ID no. 236111 (SEQ ID NO:1125), Ceres CLONE ID no. 285598 (SEQ IDNO: 1127), Ceres CLONE ID no. 225881 (SEQ ID NO: 1129), Ceres CLONE IDno. 1811383 (SEQ ID NO: 1133), Public GI ID no. 49388268 (SEQ ID NO:1135), Public GI ID no. 125590268 (SEQ ID NO: 1136), Public GI ID no.115444009 (SEQ ID NO:1137), Public GI ID no. 115447993 (SEQ ID NO:1138),Ceres ANNOT ID no. 6033842 (SEQ ID NO: 1141), Ceres ANNOT ID no. 6029952(SEQ ID NO:1143), Ceres ANNOT ID no. 6035837 (SEQ ID NO:1145), CeresANNOT ID no. 6035830 (SEQ ID NO: 1147), Ceres ANNOT ID no. 6029981 (SEQID NO: 1149), and sequences identified as functional homologs of thesequences of FIG. 13, as set forth in the sequence listing. In somecases, a functional homolog of SEQ ID NO:1047 has an amino acid sequencewith at least 40% sequence identity, e.g., 50%, 52%, 56%, 59%, 61%, 65%,70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to theamino acid sequence set forth in SEQ ID NO:1047.

Amino acid sequences of functional homologs of the polypeptide set forthin SEQ ID NO: 1151 are provided in FIG. 14. Such functional homologsinclude Ceres CLONE ID no. 1851526 (SEQ ID NO: 1155), Ceres ANNOT ID no.1486769 (SEQ ID NO: 1172). Public GI ID no. 83032232 (SEQ ID NO:1209),Ceres CLONE ID no. 1620420 (SEQ ID NO:1211), Public GI ID no. 92892428(SEQ ID NO:1215), Ceres CLONE ID no. 884742 (SEQ ID NO:1223), CeresCLONE ID no. 1821559 (SEQ ID NO:1246), Public GI ID no. 51535021 (SEQ IDNO:1258), Public GI ID no. 113205304 (SEQ ID NO:1263), and Public GI IDno. 37719051 (SEQ ID NO:1264). Other functional homologs of SEQ IDNO:1151 include Ceres CLONE ID no. 1918070 (SEQ ID NO: 1153), CeresCLONE ID no. 1948426 (SEQ ID NO: 1157), Ceres CLONE ID no. 1937875 (SEQID NO: 1159), Ceres CLONE ID no. 100056542 (SEQ ID NO:1160), Public GIID no. 5731257 (SEQ ID NO:1161), Ceres CLONE ID no. 100058043 (SEQ IDNO: 1162), Ceres CLONE ID no. 1838288 (SEQ ID NO:1164), Ceres CLONE IDno. 1793597 (SEQ ID NO:1166), Ceres ANNOT ID no. 1543031 (SEQ ID NO:1168), Ceres ANNOT ID no. 1489643 (SEQ ID NO: 1170), Ceres ANNOT ID no.1479721 (SEQ ID NO:1174), Ceres ANNOT ID no. 1449170 (SEQ ID NO: 1176),Ceres ANNOT ID no. 1493696 (SEQ ID NO:1178), Ceres ANNOT ID no. 1543534(SEQ ID NO:1180), Ceres ANNOT ID no. 1440815 (SEQ ID NO: 1182), CeresANNOT ID no. 1490137 (SEQ ID NO: 1184), Ceres ANNOT ID no. 1451054 (SEQID NO:1186), Ceres ANNOT ID no. 1456669 (SEQ ID NO:1188), Ceres ANNOT IDno. 1509865 (SEQ ID NO:1190), Ceres ANNOT ID no. 1447910 (SEQ IDNO:1192), Ceres ANNOT ID no. 1471068 (SEQ ID NO:1194), Ceres ANNOT IDno. 1504118 (SEQ ID NO:1196), Ceres CLONE ID no. 1343621 (SEQ ID NO:1198), Public GI ID no. 15218305 (SEQ ID NO: 1199), Public GI ID no.15219640 (SEQ ID NO:1200), Public GI ID no. 18409345 (SEQ ID NO:1201),Public GI ID no. 6522545 (SEQ ID NO:1202), Public GI ID no. 15237274(SEQ ID NO:1203), Public GI ID no. 26452377 (SEQ ID NO:1204), CeresCLONE ID no. 33629 (SEQ ID NO:1206), Ceres CLONE ID no. 1064407 (SEQ IDNO:1208), Ceres CLONE ID no. 1656310 (SEQ ID NO:1213), Public GI ID no.92885257 (SEQ ID NO:1214), Public GI ID no. 92868571 (SEQ ID NO:1216),Public GI ID no. 53689778 (SEQ ID NO:1217), Ceres CLONE ID no. 835598(SEQ ID NO:1219), Ceres CLONE ID no. 575649 (SEQ ID NO:1221), CeresCLONE ID no. 376567 (SEQ ID NO:1225), Ceres CLONE ID no. 1284191 (SEQ IDNO:1227), Ceres CLONE ID no. 367175 (SEQ ID NO:1229), Ceres CLONE ID no.100748296 (SEQ ID NO:1230), Ceres CLONE ID no. 1597176 (SEQ ID NO:1232),Ceres CLONE ID no. 375636 (SEQ ID NO:1234), Ceres CLONE ID no. 288123(SEQ ID NO:1236), Ceres CLONE ID no. 303582 (SEQ ID NO:1238), CeresCLONE ID no. 1604759 (SEQ ID NO:1240). Ceres CLONE ID no. 1955192 (SEQID NO:1242). Ceres CLONE ID no. 2008687 (SEQ ID NO:1244), Ceres CLONE IDno. 1995843 (SEQ ID NO:1248), Ceres CLONE ID no. 2008591 (SEQ IDNO:1250), Ceres CLONE ID no. 2046826 (SEQ ID NO:1252), Ceres CLONE IDno. 1985573 (SEQ ID NO:1254), Public GI ID no. 125541129 (SEQ IDNO:1255). Public GI ID no. 125528922 (SEQ ID NO:1256), Public GI ID no.115487590 (SEQ ID NO:1257), Public GI ID no. 115448671 (SEQ ID NO:1259),Public GI ID no. 125596564 (SEQ ID NO:1260), Public GI ID no. 125573161(SEQ ID NO:1261), Public GI ID no. 48716463 (SEQ ID NO:1262), CeresANNOT ID no. 6054246 (SEQ ID NO:1266), Ceres ANNOT ID no. 6086570 (SEQID NO:1268), Ceres ANNOT ID no. 6024957 (SEQ ID NO:1270), Ceres ANNOT IDno. 6016867 (SEQ ID NO:1272), Ceres ANNOT ID no. 6091369 (SEQ IDNO:1274), and sequences identified as functional homologs of thesequences of FIG. 14, as set forth in the sequence listing. In somecases, a functional homolog of SEQ ID NO:1151 has an amino acid sequencewith at least 40% sequence identity, e.g., 50%, 52%, 56%, 59%, 61%, 65%,70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to theamino acid sequence set forth in SEQ ID NO:1151.

Amino acid sequences of functional homologs of the polypeptide set forthin SEQ ID NO:1277 are provided in FIG. 15. Such functional homologsinclude Ceres CLONE ID no. 1926352 (SEQ ID NO:1279), Ceres ANNOT ID no.1448905 (SEQ ID NO:1285), Public GI ID no. 15236865 (SEQ ID NO:1294),Ceres CLONE ID no. 934771 (SEQ ID NO:1301), Ceres CLONE ID no. 338386(SEQ ID NO:1303), Ceres CLONE ID no. 1780691 (SEQ ID NO:1317), andPublic GI ID no. 115464819 (SEQ ID NO:1326). Other functional homologsof SEQ ID NO:1277 include Ceres CLONE ID no. 1848576 (SEQ ID NO:1281),Ceres CLONE ID no. 1981528 (SEQ ID NO:1283), Ceres ANNOT ID no. 1465978(SEQ ID NO:1287), Ceres ANNOT ID no. 1504997 (SEQ ID NO:1289), CeresANNOT ID no. 1451909 (SEQ ID NO:1291). Ceres ANNOT ID no. 1461635 (SEQID NO:1293), Public GI ID no. 18397400 (SEQ ID NO:1295), Ceres CLONE IDno. 16226 (SEQ ID NO:1297), Public GI ID no. 18411823 (SEQ ID NO:1298),Public GI ID no. 15219845 (SEQ ID NO:1299), Ceres CLONE ID no. 1276710(SEQ ID NO:1305), Ceres CLONE ID no. 1479310 (SEQ ID NO:1307), CeresCLONE ID no. 376230 (SEQ ID NO:1309), Ceres CLONE ID no. 1290713 (SEQ IDNO:1311), Ceres CLONE ID no. 321681 (SEQ ID NO:1313), Ceres CLONE ID no.1869072 (SEQ ID NO:1315), Ceres CLONE ID no. 1818502 (SEQ ID NO:1319),Ceres CLONE ID no. 1750477 (SEQ ID NO:1321), Public GI ID no. 125552947(SEQ ID NO:1322), Public GI ID no. 125527862 (SEQ ID NO:1323), Public GIID no. 125543660 (SEQ ID NO:1324), Public GI ID no. 125528123 (SEQ IDNO:1325), Public GI ID no. 115440195 (SEQ ID NO:1327), Public GI ID no.115452717 (SEQ ID NO:1328), Public GI ID no. 115440629 (SEQ ID NO:1329),Public GI ID no. 115464599 (SEQ ID NO:1330), Public GI ID no. 20161462(SEQ ID NO:1331). Public GI ID no. 125586076 (SEQ ID NO:1332), CeresCLONE ID no. 1823216 (SEQ ID NO:1334), Ceres ANNOT ID no. 6040230 (SEQID NO:1336), Ceres ANNOT ID no. 6015489 (SEQ ID NO:1338), Ceres ANNOT IDno. 6042890 (SEQ ID NO:1340), Ceres ANNOT ID no. 6040033 (SEQ IDNO:1342). Ceres ANNOT ID no. 6018414 (SEQ ID NO:1344), and sequencesidentified as functional homologs of the sequences of FIG. 15, as setforth in the sequence listing. In some cases, a functional homolog ofSEQ ID NO:1277 has an amino acid sequence with at least 40% sequenceidentity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80/6, 85%, 90%,95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence setforth in SEQ ID NO:1277.

Amino acid sequences of functional homologs of the polypeptide set forthin SEQ ID NO:1347 are provided in FIG. 16. Such functional homologsinclude Ceres CLONE ID no. 285028 (SEQ ID NO:1419), Ceres CLONE ID no.100969565 (SEQ ID NO:1422), Public GI ID no. 1352057 (SEQ ID NO:1427),Ceres ANNOT ID no. 1453784 (SEQ ID NO:1429), Public GI ID no. 452777(SEQ ID NO:1430), and Public GI ID no. 92873297 (SEQ ID NO:1431). Otherfunctional homologs of SEQ ID NO:1347 include Ceres ANNOT ID no. 1452612(SEQ ID NO:1349), Ceres CLONE ID no. 520455 (SEQ ID NO:1351), Public GIID no. 75271810 (SEQ ID NO:1352), Public GI ID no. 115489446 (SEQ IDNO:1353), Ceres CLONE ID no. 499878 (SEQ ID NO:1355), Ceres ANNOT ID no.1491840 (SEQ ID NO:1357), Public GI ID no. 125587204 (SEQ ID NO:1358),Ceres CLONE ID no. 320997 (SEQ ID NO:1360), Ceres ANNOT ID no. 1455585(SEQ ID NO:1362), Ceres ANNOT TD no. 1499460 (SEQ ID NO:1364), CeresCLONE ID no. 334484 (SEQ ID NO:1366), Ceres CLONE ID no. 100819481 (SEQID NO:1367), Public GI ID no. 115462401 (SEQ ID NO:1368), Ceres CLONE IDno. 1448136 (SEQ ID NO:1370), Ceres CLONE ID no. 277751 (SEQ IDNO:1372), Ceres ANNOT ID no. 1491839 (SEQ ID NO:1374), Ceres CLONE IDno. 100913241 (SEQ ID NO:1375), Ceres CLONE ID no. 1053224 (SEQ IDNO:1377), Ceres CLONE ID no. 425766 (SEQ ID NO:1379), Ceres CLONE ID no.485480 (SEQ ID NO:1381), Ceres CLONE ID no. 474845 (SEQ ID NO:1383),Ceres CLONE ID no. 354561 (SEQ ID NO:1385), Ceres CLONE ID no. 540858(SEQ ID NO:1387), Ceres CLONE ID no. 2032994 (SEQ ID NO:1389), CeresCLONE ID no. 2015315 (SEQ ID NO:1391), Ceres CLONE ID no. 2016149 (SEQID NO:1393), Ceres CLONE ID no. 1922843 (SEQ ID NO:1395), Ceres CLONE IDno. 2000263 (SEQ ID NO:1397), Ceres CLONE ID no. 1943510 (SEQ IDNO:1399), Ceres CLONE ID no. 1835498 (SEQ ID NO:1401), Ceres CLONE IDno. 101116694 (SEQ ID NO:1402). Ceres CLONE ID no. 1930596 (SEQ IDNO:1404), Ceres CLONE ID no. 846036 (SEQ ID NO:1406), Ceres CLONE ID no.941614 (SEQ ID NO:1408), Ceres CLONE ID no. 238788 (SEQ ID NO:1410),Public GI ID no. 125554220 (SEQ ID NO:1411), Public GI ID no. 125559895(SEQ ID NO:1412), Public GI ID no. 75252070 (SEQ ID NO:1413), Public GIID no. 115466632 (SEQ ID NO:1414). Public GI ID no. 125541525 (SEQ IDNO:1415), Ceres CLONE ID no. 1805110 (SEQ ID NO:1417), Ceres CLONE IDno. 1725309 (SEQ ID NO:1421), Ceres CLONE ID no. 100861679 (SEQ IDNO:1423), Public GI ID no. 75226278 (SEQ ID NO:1424), Public GI ID no.125525030 (SEQ ID NO:1425). Public GI ID no. 115435474 (SEQ ID NO:1426),Ceres CLONE ID no. 1728516 (SEQ ID NO:1433), Public GI ID no. 115467910(SEQ ID NO:1434), Public GI ID no. 15239950 (SEQ ID NO:1435), Public GIID no. 4887012 (SEQ ID NO:1436), Ceres ANNOT ID no. 1478544 (SEQ IDNO:1438), Public GI ID no. 90811713 (SEQ ID NO:1439). Public GI ID no.25989504 (SEQ ID NO:1440), Ceres CLONE ID no. 1113354 (SEQ ID NO:1442),Ceres CLONE ID no. 1113630 (SEQ ID NO:1444), Ceres ANNOT ID no. 6072030(SEQ ID NO:1446), Ceres ANNOT ID no. 6025654 (SEQ ID NO:1448), CeresANNOT ID no. 6091150 (SEQ ID NO:1450), Ceres ANNOT ID no. 6100390 (SEQID NO:1452), and sequences identified as functional homologs of thesequences of FIG. 16, as set forth in the sequence listing. In somecases, a functional homolog of SEQ ID NO:1347 has an amino acid sequencewith at least 40% sequence identity, e.g., 50%, 52%, 56%, 59%, 61%, 65%,70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to theamino acid sequence set forth in SEQ ID NO:1347.

Amino acid sequences of functional homologs of the polypeptide set forthin SEQ ID NO:1457 are provided in FIG. 17. Such functional homologsinclude Ceres CLONE ID no. 1924904 (SEQ ID NO:1460), Ceres ANNOT ID no.1543346 (SEQ ID NO:1462), Public GI ID no. 18396338 (SEQ ID NO:1467),Ceres CLONE ID no. 833872 (SEQ ID NO:1471), Ceres CLONE ID no. 1579587(SEQ ID NO:1475), Ceres CLONE ID no. 1786411 (SEQ ID NO:1477), andPublic GI ID no. 108864370 (SEQ ID NO:1480). Other functional homologsof SEQ ID NO:1457 include SEQ ID NO:1458. Ceres ANNOT ID no. 1532932(SEQ ID NO:1464). Ceres ANNOT ID no. 1489955 (SEQ ID NO:1466), Public GIID no. 4928917 (SEQ ID NO:1468), Public GI ID no. 6728979 (SEQ IDNO:1469), Ceres CLONE ID no. 285780 (SEQ ID NO:1473), Public GI ID no.125528863 (SEQ ID NO:1478), Public GI ID no. 125536365 (SEQ ID NO:1479).Public GI ID no. 108864369 (SEQ ID NO:1481), Public GI ID no. 115488274(SEQ ID NO:1482), Public GI ID no. 125577099 (SEQ ID NO:1483), Public GIID no. 125573110 (SEQ ID NO:1484), Public GI ID no. 124359159 (SEQ IDNO:1485), Public GI ID no. 62901479 (SEQ ID NO:1486), Ceres ANNOT ID no.6016783 (SEQ ID NO:1488), Ceres ANNOT ID no. 6020759 (SEQ ID NO:1490),Ceres ANNOT ID no. 6028676 (SEQ ID NO:1492), Ceres ANNOT ID no. 6028677(SEQ ID NO:1494), and sequences identified as functional homologs of thesequences of FIG. 17, as set forth in the sequence listing. In somecases, a functional homolog of SEQ ID NO:1457 has an amino acid sequencewith at least 40% sequence identity, e.g., 50%, 52%, 56%, 59%, 61%, 65%,70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to theamino acid sequence set forth in SEQ ID NO:1457.

Amino acid sequences of functional homologs of the polypeptide set forthin SEQ ID NO:1497 are provided in FIG. 18. Such functional homologsinclude Ceres ANNOT ID no. 1443463 (SEQ ID NO:1499), Public GI ID no.13605525 (SEQ ID NO:1502). Public GI ID no. 94965681 (SEQ ID NO:1506),and Public GI ID no. 28201254 (SEQ ID NO:1512). Other functionalhomologs of SEQ ID NO:1497 include Ceres ANNOT ID no. 1504954 (SEQ IDNO:1501), Public GI ID no. 2499553 (SEQ ID NO:1503), Public GI ID no.738308 (SEQ ID NO:1504). Public GI ID no. 4325368 (SEQ ID NO:1505),Ceres CLONE ID no. 919923 (SEQ ID NO:1508), Ceres CLONE ID no. 1659764(SEQ ID NO:1510), Public GI ID no. 125539984 (SEQ ID NO:1511), Public GIID no. 21740729 (SEQ ID NO:1513), Public GI ID no. 115458700 (SEQ IDNO:1514), Public GI ID no. 125590574 (SEQ ID NO:1515), Public GI ID no.16444957 (SEQ ID NO:1516), Ceres CLONE ID no. 1784494 (SEQ ID NO:1518),Public GI ID no. 77963980 (SEQ ID NO:1519), Public GI ID no. 124361190(SEQ ID NO:1520). Public GI ID no. 37725007 (SEQ ID NO:1521), Public GIID no. 45935258 (SEQ ID NO:1522), Public GI ID no. 15559008 (SEQ IDNO:1523), Public GI ID no. 38037416 (SEQ ID NO:1524), Public GI ID no.77963974 (SEQ ID NO:1525), Ceres ANNOT ID no. 6112581 (SEQ ID NO:1527),Public GI ID no. 56553448 (SEQ ID NO:1528), Public GI ID no. 23506659(SEQ ID NO:1529), Ceres ANNOT ID no. 6118060 (SEQ ID NO:1531), Public GIID no. 46446306 (SEQ ID NO:1532), Public GI ID no. 114321405 (SEQ IDNO:1533), Public GI TD no. 83858274 (SEQ ID NO:1534). Public GI ID no.154250969 (SEQ ID NO:1535), Public GI ID no. 83594235 (SEQ ID NO:1536),and sequences identified as functional homologs of the sequences of FIG.18, as set forth in the sequence listing. In some cases, a functionalhomolog of SEQ ID NO:1497 has an amino acid sequence with at least 40%sequence identity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%,85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acidsequence set forth in SEQ ID NO:1497.

Amino acid sequences of functional homologs of the polypeptide set forthin SEQ ID NO:1587 are provided in FIG. 19. Such functional homologsinclude Ceres CLONE ID no. 1839577 (SEQ ID NO:1589), Ceres ANNOT ID no.1491567 (SEQ ID NO:1591), Ceres CLONE ID no. 574505 (SEQ ID NO:1596),Public GI ID no. 56117815 (SEQ ID NO:1597), Public GI ID no. 92874021(SEQ ID NO:1603), Public GI ID no. 123684 (SEQ ID NO:1605), Public GI IDno. 5821136 (SEQ ID NO:1606), Ceres CLONE ID no. 283366 (SEQ IDNO:1609), Public GI ID no. 16118447 (SEQ ID NO:1612), and Public GI IDno. 125562434 (SEQ ID NO:1614). Other functional homologs of SEQ IDNO:1587 include Ceres ANNOT ID no. 1438739 (SEQ ID NO:1593), Public GIID no. 89274218 (SEQ ID NO:1594), Public GI ID no. 115521211 (SEQ IDNO:1598), Public GI ID no. 115521213 (SEQ ID NO:1599), Public GI ID no.115521217 (SEQ ID NO:1600), Public GI ID no. 115521209 (SEQ ID NO:1601),Public GI ID no. 115521215 (SEQ ID NO:1602), Public GI ID no. 11386827(SEQ ID NO:1604), Public GI ID no. 25052685 (SEQ ID NO:1607), CeresCLONE ID no. 1440437 (SEQ ID NO:1611), Public GI ID no. 125564440 (SEQID NO:1613). Public GI ID no. 116309817 (SEQ ID NO:1615), Public GI IDno. 125549382 (SEQ ID NO:1616), Public GI ID no. 52077317 (SEQ IDNO:1617). Public GI ID no. 115477655 (SEQ ID NO:1618), Public GI ID no.42408097 (SEQ ID NO:1619), Public GI ID no. 115459982 (SEQ ID NO:1620),Public GI ID no. 33591096 (SEQ ID NO:1621), Ceres CLONE ID no. 484753(SEQ ID NO:1623), Ceres ANNOT ID no. 6035291 (SEQ ID NO:1625), andsequences identified as functional homologs of the sequences of FIG. 19,as set forth in the sequence listing. In some cases, a functionalhomolog of SEQ ID NO:1587 has an amino acid sequence with at least 40%sequence identity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%,85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acidsequence set forth in SEQ ID NO:1587.

Amino acid sequences of functional homologs of the polypeptide set forthin SEQ ID NO:1635 are provided in FIG. 20. Such functional homologsinclude Ceres ANNOT ID no. 1508307 (SEQ ID NO:1637), Public GI ID no.1495267 (SEQ ID NO:1642), Public GI ID no. 87241310 (SEQ ID NO:1644),Ceres CLONE ID no. 938390 (SEQ ID NO:1646), Ceres CLONE ID no. 272338(SEQ ID NO:1648), Ceres CLONE ID no. 1993510 (SEQ ID NO:1650), Public GIID no. 125563862 (SEQ ID NO:1651), and Public GI ID no. 125605833 (SEQID NO:1653). Other functional homologs of SEQ ID NO:1635 include PublicGI ID no. 6899919 (SEQ ID NO:1632), Ceres ANNOT ID no. 1455110 (SEQ IDNO:1639), Ceres ANNOT ID no. 1525218 (SEQ ID NO:1641), Public GI ID no.15231597 (SEQ ID NO:1643). Public GI ID no. 125548147 (SEQ ID NO:1652),Public GI ID no. 51091343 (SEQ ID NO:1654), Public GI ID no. 115479355(SEQ ID NO:1655), Ceres ANNOT ID no. 6042086 (SEQ ID NO:1657), CeresANNOT ID no. 6029903 (SEQ ID NO:1659), and sequences identified asfunctional homologs of the sequences of FIG. 20, as set forth in thesequence listing. In some cases, a functional homolog of SEQ ID NO:1635has an amino acid sequence with at least 40% sequence identity, e.g.,50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80/0, 85%, 90%, 95%, 97%, 98%,or 99% sequence identity, to the amino acid sequence set forth in SEQ IDNO:1635.

Amino acid sequences of functional homologs of the polypeptide set forthin SEQ ID NO:1540 are provided in FIG. 21. Such functional homologsinclude Ceres CLONE ID no. 1943265 (SEQ ID NO:1543), Ceres ANNOT ID no.1454522 (SEQ ID NO:1547), Public GI ID no. 31323447 (SEQ ID NO:1556),Ceres CLONE ID no. 1583941 (SEQ ID NO:1561), Ceres CLONE ID no. 1792942(SEQ ID NO:1563), Public GI ID no. 77548772 (SEQ ID NO:1565), and PublicGI ID no. 84453182 (SEQ ID NO:1567). Other functional homologs of SEQ IDNO:1540 include Public GI ID no. 31746344 (SEQ ID NO:1541), Ceres CLONEID no. 1926640 (SEQ ID NO:1545), Ceres ANNOT ID no. 1475125 (SEQ IDNO:1549), Ceres ANNOT ID no. 1439653 (SEQ ID NO:1551), Ceres ANNOT IDno. 1461995 (SEQ ID NO:1553), Public GI ID no. 13877517 (SEQ IDNO:1554). Public GI ID no. 7239157 (SEQ ID NO:1555), Public GI ID no.22652125 (SEQ ID NO:1557), Public GI ID no. 22652115 (SEQ ID NO:1558),Public GI ID no. 22652117 (SEQ ID NO:1559), Public GI TD no. 125535858(SEQ ID NO:1564), Public GI ID no. 125578581 (SEQ ID NO:1566), Public GIID no. 13752407 (SEQ ID NO:1568), Ceres ANNOT ID no. 6098817 (SEQ IDNO:1570), Ceres ANNOT ID no. 6039430 (SEQ ID NO:1572), Ceres ANNOT IDno. 6068141 (SEQ ID NO:1574), Ceres ANNOT ID no. 6033916 (SEQ IDNO:1576), Ceres ANNOT ID no. 6034399 (SEQ ID NO:1578), Ceres ANNOT IDno. 6068617 (SEQ ID NO:1580), Ceres ANNOT ID no. 6026318 (SEQ IDNO:1582), Ceres ANNOT ID no. 6107650 (SEQ ID NO:1584), and sequencesidentified as functional homologs of the sequences of FIG. 21, as setforth in the sequence listing. In some cases, a functional homolog ofSEQ ID NO:1540 has an amino acid sequence with at least 40% sequenceidentity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%,95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence setforth in SEQ ID NO:1540.

Amino acid sequences of functional homologs of the polypeptide set forthin SEQ ID NO:538 are provided in FIG. 22. Such functional homologsinclude Public GI ID no. 5731739 (SEQ ID NO:539), Ceres ANNOT ID no.1538045 (SEQ ID NO:541), Public GI ID no. 29467479 (SEQ ID NO:542),Public GI ID no. 133921974 (SEQ ID NO:543), Public GI ID no. 113197027(SEQ ID NO:544), Public GI ID no. 92879277 (SEQ ID NO:545), Public GI IDno. 45935260 (SEQ ID NO:546), Public GI ID no. 8101444 (SEQ ID NO:547),Public GI ID no. 78217443 (SEQ ID NO:548), and Public GI ID no. 28372347(SEQ ID NO:549). Other functional homologs of SEQ ID NO:538 includePublic GI ID no. 16416405 (SEQ ID NO:550), Ceres ANNOT ID no. 1484634(SEQ ID NO:552), Ceres ANNOT ID no. 1451869 (SEQ ID NO:554), Public GIID no. 25407462 (SEQ ID NO:555), Public GI TD no. 29467481 (SEQ IDNO:556), Public GI ID no. 29467477 (SEQ ID NO:557), Public GI ID no.45935264 (SEQ ID NO:558), Public GI ID no. 5524201 (SEQ ID NO:559),Public GI ID no. 78217441 (SEQ ID NO:560), Public GI ID no. 3551221 (SEQID NO:561), Public GI ID no. 3551219 (SEQ ID NO:562), Public GI ID no.23954324 (SEQ ID NO:563), Public GI ID no. 125582937 (SEQ ID NO:564),Public GI ID no. 83764373 (SEQ ID NO:565), Ceres ANNOT ID no. 6045327(SEQ ID NO:567), and sequences identified as functional homologs of thesequences of FIG. 22, as set forth in the sequence listing. In somecases, a functional homolog of SEQ ID NO:538 has an amino acid sequencewith at least 40% sequence identity, e.g., 50%, 52%, 56%, 59%, 61%, 65%,70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to theamino acid sequence set forth in SEQ ID NO:538.

Amino acid sequences of functional homologs of the polypeptide set forthin SEQ ID NO:606 are provided in FIG. 23. Such functional homologsinclude Public GI ID no. 92873064 (SEQ ID NO:607), Public GI ID no.37051125 (SEQ ID NO:608), and Public GI ID no. 112363376 (SEQ IDNO:609). Other functional homologs of SEQ ID NO:606 include Ceres CLONEID no. 1938524 (SEQ ID NO:611), Ceres ANNOT ID no. 1473601 (SEQ IDNO:613), Ceres ANNOT ID no. 1468397 (SEQ ID NO:615), Public GI ID no.21554185 (SEQ ID NO:616), Public GI ID no. 18424330 (SEQ ID NO:617),Public GI ID no. 8885571 (SEQ ID NO:618), Ceres CLONE ID no. 20852 (SEQID NO:620), Public GI ID no. 21553763 (SEQ ID NO:621), Public GI ID no.18401763 (SEQ ID NO:622), Ceres CLONE ID no. 16423 (SEQ ID NO:624),Public GI ID no. 112363380 (SEQ ID NO:625), Public GI ID no. 6092016(SEQ ID NO:626), Ceres CLONE ID no. 770468 (SEQ ID NO:628), Public GI IDno. 113205234 (SEQ ID NO:629), Ceres ANNOT ID no. 6094775 (SEQ IDNO:631), and sequences identified as functional homologs of thesequences of FIG. 23, as set forth in the sequence listing. In somecases, a functional homolog of SEQ ID NO:606 has an amino acid sequencewith at least 40% sequence identity, e.g., 50%, 52%, 56%, 59%, 61%, 65%,70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to theamino acid sequence set forth in SEQ ID NO:606.

Amino acid sequences of functional homologs of the polypeptide set forthin SEQ ID NO:570 are provided in FIG. 24. Such functional homologsinclude Ceres CLONE ID no. 1919714 (SEQ ID NO:572), Ceres ANNOT ID no.1443290 (SEQ ID NO:574), Ceres CLONE ID no. 1042157 (SEQ ID NO:576),Ceres CLONE ID no. 1384304 (SEQ ID NO:578), and Public GI ID no.115464375 (SEQ ID NO:579).

Other functional homologs of SEQ ID NO:570 include Ceres CLONE ID no.100028078 (SEQ ID NO:580), Ceres ANNOT ID no. 1452096 (SEQ ID NO:582),Ceres ANNOT ID no. 1503869 (SEQ ID NO:584), Ceres ANNOT ID no. 1525651(SEQ ID NO:586), Ceres CLONE ID no. 1645639 (SEQ ID NO:588), Ceres CLONEID no. 603237 (SEQ ID NO:590), Ceres CLONE ID no. 340925 (SEQ IDNO:592), Ceres CLONE ID no. 293238 (SEQ ID NO:594), Ceres CLONE ID no.483742 (SEQ ID NO:596), Ceres CLONE ID no. 1460255 (SEQ ID NO:598),Ceres CLONE TD no. 1400107 (SEQ ID NO:600), Public GI ID no. 115440865(SEQ ID NO:601), Ceres ANNOT ID no. 6016008 (SEQ ID NO:603), andsequences identified as functional homologs of the sequences of FIG. 24,as set forth in the sequence listing. In some cases, a functionalhomolog of SEQ ID NO:570 has an amino acid sequence with at least 40%sequence identity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%,85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acidsequence set forth in SEQ ID NO:570.

The identification of conserved regions in an SD+EODFR and/or low lighttolerance polypeptide facilitates production of variants of SD+EODFRand/or low light tolerance polypeptides. Variants of SD+EODFR and/or lowlight tolerance polypeptides typically have 10 or fewer conservativeamino acid substitutions within the primary amino acid sequence, e.g., 7or fewer conservative amino acid substitutions, 5 or fewer conservativeamino acid substitutions, or between 1 and 5 conservative substitutions.A useful variant polypeptide can be constructed based on one of thealignments set forth in FIGS. 1-24. Such a polypeptide includes theconserved regions, arranged in the order depicted in the Figure fromamino-terminal end to carboxy-terminal end. Such a polypeptide may alsoinclude zero, one, or more than one amino acid in positions marked bydashes. When no amino acids are present at positions marked by dashes,the length of such a polypeptide is the sum of the amino acid residuesin all conserved regions. When amino acids are present at all positionsmarked by dashes, such a polypeptide has a length that is the sum of theamino acid residues in all conserved regions and all dashes.

D. Functional Homologs Identified by HMMER

In some embodiments, useful SD+EODFR and/or low light tolerancepolypeptides include those that fit a Hidden Markov Model based on thepolypeptides set forth in any one of FIGS. 1-24. A Hidden Markov Model(HMM) is a statistical model of a consensus sequence for a group offunctional homologs. See. Durbin et al., Biological Sequence Analysis:Probabilistic Models of Proteins and Nucleic Acids, Cambridge UniversityPress, Cambridge, UK (1998). An HMM is generated by the program HMMER2.3.2 with default program parameters, using the sequences of the groupof functional homologs as input. The multiple sequence alignment isgenerated by ProbCons (Do et al., Genome Res., 15(2):330-40 (2005))version 1.11 using a set of default parameters: -c, - -consistency REPSof 2; -ir, - -iterative-refinement REPS of 100; -pre, - -pre-trainingREPS of 0. ProbCons is a public domain software program provided byStanford University.

The default parameters for building an HMM (hmmbuild) are as follows:the default “architecture prior” (archpri) used by MAP architectureconstruction is 0.85, and the default cutoff threshold (idlevel) used todetermine the effective sequence number is 0.62. HMMER 2.3.2 wasreleased Oct. 3, 2003 under a GNU general public license, and isavailable from various sources on the World Wide Web such ashmmer.janelia.org; hmmer.wustl.edu; and fr.com/hmmer232/. Hmmbuildoutputs the model as a text file.

The HMM for a group of functional homologs can be used to determine thelikelihood that a candidate SD+EODFR and/or low light tolerancepolypeptide sequence is a better fit to that particular HMM than to anull HMM generated using a group of sequences that are not structurallyor functionally related. The likelihood that a candidate polypeptidesequence is a better fit to an HMM than to a null HMM is indicated bythe HMM bit score, a number generated when the candidate sequence isfitted to the HMM profile using the HMMER hmmsearch program. Thefollowing default parameters are used when running hmmsearch: thedefault E-value cutoff (E) is 10.0, the default bit score cutoff (T) isnegative infinity, the default number of sequences in a database (Z) isthe real number of sequences in the database, the default E-value cutofffor the per-domain ranked hit list (domE) is infinity, and the defaultbit score cutoff for the per-domain ranked hit list (domT) is negativeinfinity. A high HMM bit score indicates a greater likelihood that thecandidate sequence carries out one or more of the biochemical orphysiological function(s) of the polypeptides used to generate the HMM.A high HMM bit score is at least 20, and often is higher. Slightvariations in the HMM bit score of a particular sequence can occur dueto factors such as the order in which sequences are processed foralignment by multiple sequence alignment algorithms such as the ProbConsprogram. Nevertheless, such HMM bit score variation is minor.

The SD+EODFR and/or low light tolerance polypeptides discussed below fitthe indicated HMM with an HMM bit score greater than 20 (e.g., greaterthan 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, or 500). In someembodiments, the HMM bit score of an SD+EODFR and/or low light tolerancepolypeptide discussed below is about 50%, 60%, 70%, 80%, 90%, or 95% ofthe HMM bit score of a functional homolog provided in the SequenceListing. In some embodiments, an SD+EODFR and/or low light tolerancepolypeptide discussed below fits the indicated HMM with an HMM bit scoregreater than 20, and has a domain indicative of an SD+EODFR and/or lowlight tolerance polypeptide. In some embodiments, an SD+EODFR and/or lowlight tolerance polypeptide discussed below fits the indicated HMM withan HMM bit score greater than 20, and has 70% or greater sequenceidentity (e.g., 75%, 80%, 85%, 90%, 95%, or 100% sequence identity) toan amino acid sequence shown in any one of FIGS. 1-24.

Polypeptides are shown in the sequence listing that have HMM bit scoresgreater than 170 when fitted to an HMM generated from the amino acidsequences set forth in FIG. 1. Such polypeptides include At4g37295 (SEQID NO:3), Ceres CLONE ID no. 1844057 (SEQ ID NO:7), Ceres ANNOT ID no.1469148 (SEQ ID NO:22), Public GI ID no. 18390998 (SEQ ID NO:25), CeresCLONE ID no. 1065656 (SEQ ID NO:32), Ceres CLONE ID no. 1652677 (SEQ IDNO:36), Public GI ID no. 92874556 (SEQ ID NO:49), Ceres CLONE ID no.1329161 (SEQ ID NO:53), Ceres CLONE ID no. 1030378 (SEQ ID NO:55), CeresCLONE ID no. 1413787 (SEQ ID NO:57), Public GI ID no. 125543598 (SEQ IDNO:60), Ceres CLONE ID no. 1793691 (SEQ ID NO:5), Ceres CLONE ID no.1933784 (SEQ ID NO:9), Ceres CLONE ID no. 100030408 (SEQ ID NO:10),Ceres CLONE ID no. 1837059 (SEQ ID NO:12), Ceres CLONE ID no. 1793801(SEQ ID NO:14), Ceres CLONE ID no. 1855480 (SEQ ID NO:16), Ceres CLONEID no. 1915644 (SEQ ID NO:18), Ceres CLONE ID no. 1898104 (SEQ IDNO:20), Ceres ANNOT ID no. 1464241 (SEQ ID NO:24), Public GI ID no.18697627 (SEQ ID NO:26), Ceres CLONE ID no. 9391 (SEQ ID NO:28), CeresCLONE ID no. 111154 (SEQ ID NO:30), Ceres CLONE ID no. 973975 (SEQ IDNO:34), Ceres CLONE ID no. 676695 (SEQ ID NO:38), Ceres CLONE ID no.680331 (SEQ ID NO:40), Ceres CLONE ID no. 654515 (SEQ ID NO:42), CeresCLONE ID no. 626154 (SEQ ID NO:44), Ceres CLONE ID no. 710603 (SEQ IDNO:46), Ceres CLONE ID no. 648076 (SEQ ID NO:48), Ceres CLONE ID no.749439 (SEQ ID NO:51), Ceres CLONE ID no. 295936 (SEQ ID NO:59), PublicGI ID no. 125525139 (SEQ ID NO:61), Public GI ID no. 115452643 (SEQ IDNO:62), Public GI ID no. 24059889 (SEQ ID NO:63), Ceres ANNOT ID no.6012747 (SEQ ID NO:65), Ceres ANNOT ID no. 6027628 (SEQ ID NO:67), andsequences identified as functional homologs of the sequences of FIG. 1,as set forth in the sequence listing.

Polypeptides are shown in the sequence listing that have HMM bit scoresgreater than 80 when fitted to an HMM generated from the amino acidsequences set forth in FIG. 2. Such polypeptides include At2g32710 (SEQID NO:70), Ceres CLONE ID no. 1975934 (SEQ ID NO:72), Ceres ANNOT ID no.1529913 (SEQ ID NO:80), Ceres CLONE ID no. 977794 (SEQ ID NO:93), PublicGI ID no. 42362378 (SEQ ID NO:96), Public GI ID no. 23899378 (SEQ IDNO:99), Public GI ID no. 15963346 (SEQ ID NO:101), Public GI ID no.15963344+B816 (SEQ ID NO:102), Public GI ID no. 92429657 (SEQ IDNO:103), Ceres CLONE ID no. 746644 (SEQ ID NO:105), Ceres CLONE ID no.623089 (SEQ ID NO:109), Ceres CLONE ID no. 1913678 (SEQ ID NO: 115),Public GI ID no. 115450609 (SEQ ID NO:119), Ceres CLONE ID no. 1835084(SEQ ID NO:74), Ceres CLONE ID no. 1846153 (SEQ ID NO:76), Ceres CLONEID no. 1930884 (SEQ ID NO:78), Ceres ANNOT ID no. 1493858 (SEQ IDNO:82), Ceres ANNOT ID no. 1498646 (SEQ ID NO:84), Ceres ANNOT ID no.1440974 (SEQ ID NO:86), Ceres CLONE ID no. 1189183 (SEQ ID NO:88),Public GI ID no. 26450253 (SEQ ID NO:89), Public GI ID no. 15239719 (SEQID NO:90), Public GI ID no. 15230194 (SEQ ID NO:91), Ceres CLONE ID no.630905 (SEQ ID NO:95), Public GT ID no. 42362389 (SEQ ID NO:97), PublicGI TD no. 70906129 (SEQ ID NO:98), Public GI ID no. 23899381 (SEQ IDNO:100), Ceres CLONE ID no. 298166 (SEQ ID NO:107), Ceres CLONE ID no.1448390 (SEQ ID NO:111). Ceres CLONE ID no. 1734216 (SEQ ID NO:113),Public GI ID no. 125542322 (SEQ ID NO:116), Public GI ID no. 125532331(SEQ ID NO:117), Public GI ID no. 125541233 (SEQ ID NO:118), Public GIID no. 125584844 (SEQ ID NO:120), Public GI ID no. 115482472 (SEQ IDNO:121), Public GI ID no. 125575112 (SEQ ID NO:122), Ceres ANNOT ID no.6003994 (SEQ ID NO:124), Ceres ANNOT ID no. 6068427 (SEQ ID NO:126), andsequences identified as functional homologs of the sequences of FIG. 2,as set forth in the sequence listing.

Polypeptides are shown in the sequence listing that have HMM bit scoresgreater than 80 when fitted to an HMM generated from the amino acidsequences set forth in FIG. 3. Such polypeptides include Public GI IDno. 34550779 (SEQ ID NO:133), Ceres CLONE ID no. 1932235 (SEQ IDNO:137). Ceres CLONE ID no. 981738 (SEQ ID NO:201), Ceres CLONE ID no.565974 (SEQ ID NO:209), Public GI ID no. 1352058 (SEQ ID NO:231), PublicGI ID no. 11131101 (SEQ ID NO:234), Public GI ID no. 4887018 (SEQ IDNO:236), Public GI ID no. 4887018 (SEQ ID NO:236), Ceres CLONE ID no.644455 (SEQ ID NO:247), Ceres CLONE ID no. 1731500 (SEQ ID NO:270),Public GI ID no. 20269063 (SEQ ID NO:300), Public GI ID no. 50404477(SEQ ID NO:302), Public GI ID no. 62125392 (SEQ ID NO:303), Public GI IDno. 32396293 (SEQ ID NO:130), Public GI ID no. 32396299 (SEQ ID NO:131),Public GI ID no. 32396295 (SEQ ID NO:132), Ceres CLONE ID no. 1855369(SEQ ID NO:135), Ceres CLONE ID no. 1948456 (SEQ ID NO:139), Ceres CLONEID no. 1920182 (SEQ ID NO:141), Ceres CLONE ID no. 1835797 (SEQ IDNO:143), Ceres CLONE ID no. 1794204 (SEQ ID NO:145), Ceres CLONE ID no.1853542 (SEQ ID NO:147), Ceres CLONE ID no. 1838776 (SEQ ID NO:149),Ceres CLONE ID no. 1854675 (SEQ ID NO:151), Ceres CLONE ID no. 1833078(SEQ ID NO:153), Ceres CLONE ID no. 1850667 (SEQ ID NO:155). Ceres CLONEID no. 1918745 (SEQ ID NO:157), Ceres CLONE ID no. 1929487 (SEQ IDNO:159), Ceres ANNOT ID no. 1497918 (SEQ ID NO:161), Ceres ANNOT ID no.1459563 (SEQ ID NO:163), Ceres ANNOT ID no. 1452610 (SEQ ID NO:165),Ceres ANNOT ID no. 1496539 (SEQ ID NO:167), Ceres ANNOT ID no. 1498819(SEQ ID NO:169), Ceres ANNOT ID no. 1446583 (SEQ ID NO:171), Ceres ANNOTID no. 1535123 (SEQ ID NO:173), Ceres ANNOT ID no. 1463397 (SEQ IDNO:175). Ceres ANNOT ID no. 1499563 (SEQ ID NO:177), Ceres ANNOT ID no.1495753 (SEQ ID NO:179), Ceres ANNOT ID no. 1488767 (SEQ ID NO:181),Ceres ANNOT ID no. 1522920 (SEQ ID NO:185). Ceres ANNOT ID no. 1469532(SEQ ID NO:187), Public GI ID no. 15219692 (SEQ ID NO:188), Public GI IDno. 18420964 (SEQ ID NO:189). Ceres CLONE ID no. 1342080 (SEQ IDNO:191), Ceres CLONE ID no. 123105 (SEQ TD NO:193), Ceres CLONE ID no.32727 (SEQ ID NO:195), Ceres CLONE ID no. 41161 (SEQ ID NO:197), CeresCLONE ID no. 37274 (SEQ ID NO:199), Ceres CLONE ID no. 538020 (SEQ IDNO:203), Ceres CLONE ID no. 476244 (SEQ ID NO:205). Ceres CLONE ID no.1623662 (SEQ ID NO:207), Ceres CLONE ID no. 626817 (SEQ ID NO:211),Ceres CLONE ID no. 537469 (SEQ ID NO:213), Ceres CLONE ID no. 582463(SEQ ID NO:215), Ceres CLONE ID no. 1069818 (SEQ ID NO:217), Ceres CLONEID no. 511737 (SEQ ID NO:219), Ceres CLONE ID no. 565422 (SEQ IDNO:221), Ceres CLONE ID no. 514595 (SEQ ID NO:223), Ceres CLONE ID no.566396 (SEQ ID NO:225), Ceres CLONE ID no. 612705 (SEQ ID NO:227), CeresCLONE ID no. 564134 (SEQ ID NO:229), Public GI ID no. 92872146 (SEQ IDNO:230), Public GI ID no. 11131103 (SEQ ID NO:232), Public GI ID no.416641 (SEQ ID NO:233), Public GI ID no. 11131105 (SEQ ID NO:235),Public GI ID no. 4887016 (SEQ ID NO:237), Public GI ID no. 4887022 (SEQID NO:238), Public GI ID no. 81074526 (SEQ ID NO:239), Ceres CLONE IDno. 742023 (SEQ ID NO:241), Ceres CLONE ID no. 576268 (SEQ ID NO:243),Ceres CLONE ID no. 615386 (SEQ ID NO:245), Ceres CLONE ID no. 756966(SEQ ID NO:249), Ceres CLONE ID no. 1052710 (SEQ ID NO:251), Ceres CLONEID no. 697018 (SEQ ID NO:253), Ceres CLONE ID no. 618577 (SEQ IDNO:255), Ceres CLONE ID no. 935194 (SEQ ID NO:257), Ceres CLONE ID no.1557429 (SEQ ID NO:259), Ceres CLONE ID no. 305337 (SEQ ID NO:261),Ceres CLONE ID no. 100872943 (SEQ ID NO:262), Ceres CLONE ID no. 305454(SEQ ID NO:264), Ceres CLONE ID no. 1534670 (SEQ ID NO:266), Ceres CLONEID no. 207963 (SEQ ID NO:268), Public GI ID no. 20257219 (SEQ IDNO:271), Ceres CLONE ID no. 1876818 (SEQ ID NO:273), Ceres CLONE ID no.1817533 (SEQ ID NO:275), Ceres CLONE ID no. 1958631 (SEQ ID NO:277),Ceres CLONE ID no. 1963215 (SEQ ID NO:279), Ceres CLONE ID no. 1770022(SEQ ID NO:281), Ceres CLONE ID no. 1796223 (SEQ ID NO:283), Ceres CLONEID no. 2016695 (SEQ ID NO:285), Ceres CLONE ID no. 1757085 (SEQ IDNO:287), Ceres CLONE ID no. 1769256 (SEQ ID NO:289), Ceres CLONE ID no.1994871 (SEQ ID NO:291), Public GI ID no. 17154533 (SEQ ID NO:292),Public GI ID no. 125557426 (SEQ ID NO:293), Public GI ID no. 125524736(SEQ ID NO:294), Public GI ID no. 125527656 (SEQ ID NO:295), Public GIID no. 125599342 (SEQ ID NO:296), Public GI ID no. 125569626 (SEQ IDNO:297), Public GI ID no. 115465401 (SEQ ID NO:298), Public GI ID no.40539038 (SEQ ID NO:299), Public GI ID no. 20269059 (SEQ ID NO:301),Public GI ID no. 110826446 (SEQ ID NO:304), Ceres ANNOT ID no. 6029073(SEQ ID NO:306), Ceres ANNOT ID no. 6011329 (SEQ ID NO:308), Ceres ANNOTID no. 6034498 (SEQ ID NO:310). Ceres ANNOT ID no. 6095057 (SEQ IDNO:312), Ceres ANNOT ID no. 6095058 (SEQ ID NO:314), and sequencesidentified as functional homologs of the sequences of FIG. 3, as setforth in the sequence listing.

Polypeptides are shown in the sequence listing that have HMM bit scoresgreater than 200 when fitted to an HMM generated from the amino acidsequences set forth in FIG. 4. Such polypeptides include At4g03250(Ceres Seedline ME10007; SEQ ID NO:317), Ceres CLONE ID no. 1842125 (SEQID NO:319), Ceres ANNOT ID no. 1461360 (SEQ ID NO:321), Ceres CLONE IDno. 480906 (SEQ ID NO:327), Public GI ID no. 92889352 (SEQ ID NO:330),Public GI ID no. 56201850 (SEQ ID NO:330), Ceres ANNOT ID no. 1440334(SEQ ID NO:323), Ceres ANNOT ID no. 1493205 (SEQ ID NO:325), Ceres CLONEID no. 482270 (SEQ ID NO:329), Public GI ID no. 125571531 (SEQ IDNO:332), Ceres ANNOT ID no. 6042411 (SEQ ID NO:334), and sequencesidentified as functional homologs of the sequences of FIG. 4, as setforth in the sequence listing.

Polypeptides are shown in the sequence listing that have HMM bit scoresgreater than 80 when fitted to an HMM generated from the amino acidsequences set forth in FIG. 5. Such polypeptides include At2g04240 (SEQID NO:337), Ceres CLONE ID no. 952050 (SEQ ID NO:339), Public GI ID no.115477050 (SEQ ID NO:349), Public GI ID no. 87162911 (SEQ ID NO:355),Ceres CLONE ID no. 1790901 (SEQ ID NO:357), Ceres CLONE ID no. 1460088(SEQ ID NO:370), Ceres CLONE ID no. 1734065 (SEQ ID NO:393), Ceres CLONEID no. 473509 (SEQ ID NO:395), Ceres CLONE ID no. 849918 (SEQ IDNO:401), Ceres CLONE ID no. 633470 (SEQ ID NO:409), Ceres CLONE ID no.1808334 (SEQ ID NO:417), Ceres ANNOT ID no. 1525600 (SEQ ID NO:437),Ceres CLONE ID no. 1265097 (SEQ ID NO:341), Ceres CLONE ID no. 942980(SEQ ID NO:343), Public GI ID no. 37901055 (SEQ ID NO:344), Ceres CLONEID no. 1609912 (SEQ ID NO:346), Public GI ID no. 76446335 (SEQ IDNO:347), Public GI ID no. 125560204 (SEQ ID NO:348), Public GI ID no.125303087 (SEQ ID NO:350), Public GI ID no. 115460088 (SEQ ID NO:351),Public GI ID no. 125591385 (SEQ ID NO:352), Public GI ID no. 115447931(SEQ ID NO:353), Public GI ID no. 92893514 (SEQ ID NO:354), Ceres CLONEID no. 2019320 (SEQ ID NO:359), Ceres CLONE ID no. 1890013 (SEQ IDNO:361), Public GI LD no. 20340241 (SEQ ID NO:362), Ceres CLONE ID no.25801 (SEQ ID NO:364), Public GI ID no. 9743343 (SEQ ID NO:365), PublicGI ID no. 15238072 (SEQ ID NO:366), Public GI ID no. 15222553 (SEQ IDNO:367), Public GI ID no. 21554155 (SEQ ID NO:368). Ceres CLONE ID no.374439 (SEQ ID NO:372), Ceres CLONE ID no. 1465572 (SEQ ID NO:374),Ceres CLONE ID no. 1565524 (SEQ ID NO:376), Ceres CLONE ID no. 322302(SEQ ID NO:378), Ceres CLONE ID no. 101136485 (SEQ ID NO:379), CeresCLONE ID no. 1376133 (SEQ ID NO:381), Ceres CLONE ID no. 1374381 (SEQ IDNO:383), Ceres CLONE ID no. 1566473 (SEQ ID NO:385), Ceres CLONE ID no.318088 (SEQ ID NO:387), Ceres CLONE ID no. 1452604 (SEQ ID NO:389),Ceres CLONE ID no. 337906 (SEQ ID NO:391), Ceres CLONE ID no. 1662513(SEQ ID NO:397), Ceres CLONE ID no. 1662527 (SEQ ID NO:399), Ceres CLONEID no. 571184 (SEQ ID NO:403), Ceres CLONE ID no. 665689 (SEQ IDNO:405), Ceres CLONE ID no. 1365853 (SEQ ID NO:407), Ceres CLONE ID no.1052457 (SEQ ID NO:411), Ceres CLONE ID no. 579918 (SEQ ID NO:413),Ceres CLONE ID no. 863299 (SEQ ID NO:415), Ceres CLONE ID no. 1855611(SEQ ID NO:419), Ceres CLONE ID no. 1845975 (SEQ ID NO:421), Ceres CLONEID no. 1808298 (SEQ ID NO:423). Ceres CLONE ID no. 1841236 (SEQ IDNO:425), Ceres CLONE ID no. 1808269 (SEQ ID NO:427), Ceres CLONE ID no.1850628 (SEQ ID NO:429), Ceres CLONE ID no. 1846911 (SEQ ID NO:431),Ceres CLONE ID no. 1916014 (SEQ ID NO:433), Ceres CLONE ID no. 1842594(SEQ ID NO:435), Ceres ANNOT ID no. 1472192 (SEQ ID NO:439), Ceres ANNOTID no. 1447489 (SEQ ID NO:441), Ceres ANNOT ID no. 1513000 (SEQ IDNO:443), Ceres ANNOT ID no. 1438658 (SEQ ID NO:445), Ceres ANNOT ID no.1497255 (SEQ ID NO:447), Ceres ANNOT ID no. 6092104 (SEQ ID NO:449),Ceres ANNOT ID no. 6041700 (SEQ ID NO:451), Ceres ANNOT ID no. 6007297(SEQ ID NO:453), and sequences identified as functional homologs of thesequences of FIG. 5, as set forth in the sequence listing.

Polypeptides are shown in the sequence listing that have HMM bit scoresgreater than 60 when fitted to an HMM generated from the amino acidsequences set forth in FIG. 6. Such polypeptides include At5g14370 (SEQID NO:456), Public GT ID no. 58430585 (SEQ ID NO:457), Ceres CLONE IDno. 1842825 (SEQ ID NO:466). Ceres ANNOT ID no. 1449721 (SEQ ID NO:474),Public GI ID no. 41323978 (SEQ ID NO:475), Public GI ID no. 2895186 (SEQID NO:478), Public GI ID no. 22854950 (SEQ ID NO:481), Public GI ID no.116010474 (SEQ ID NO:485), Public GI ID no. 4091804 (SEQ ID NO:488),Public GI ID no. 60459257 (SEQ ID NO:494), Public GI ID no. 45544881(SEQ ID NO:496), Public GI ID no. 36789802 (SEQ ID NO:498), Public GI IDno. 92875402 (SEQ ID NO:508), Public GI ID no. 118406898 (SEQ IDNO:510), Public GI ID no. 107770485 (SEQ ID NO:511), Public GI ID no.90657642 (SEQ ID NO:536), Ceres CLONE ID no. 1569555 (SEQ ID NO:1842)Public GI ID no. 66841018 (SEQ ID NO:458), Public GI ID no. 66841020(SEQ ID NO:459), Public GI ID no. 108859343 (SEQ ID NO:460), Ceres CLONEID no. 1937613 (SEQ ID NO:462), Ceres CLONE ID no. 1834027 (SEQ IDNO:464), Ceres ANNOT ID no. 1477832 (SEQ ID NO:468), Ceres ANNOT ID no.1482536 (SEQ ID NO:470), Ceres ANNOT ID no. 1478227 (SEQ ID NO:472),Ceres CLONE ID no. 19906 (SEQ ID NO:478). Public GI ID no. 2895184 (SEQID NO:479), Public GI ID no. 2895188 (SEQ ID NO:480), Public GI ID no.11037313 (SEQ ID NO:482), Public GI ID no. 22854908 (SEQ ID NO:483),Public GI ID no. 40787165 (SEQ ID NO:484), Public GI ID no. 116010475(SEQ ID NO:486), Public GI ID no. 3341723 (SEQ ID NO:487). Public GI IDno. 4091806 (SEQ ID NO:489), Ceres CLONE ID no. 523203 (SEQ LD NO:491),Ceres CLONE ID no. 463157 (SEQ ID NO:493), Public GI ID no. 61611678(SEQ ID NO:495), Public GI ID no. 45544887 (SEQ ID NO:497), Public GI IDno. 36789793 (SEQ ID NO:481). Ceres CLONE ID no. 907473 (SEQ ID NO:501),Ceres CLONE LD no. 1674443 (SEQ ID NO:503), Ceres CLONE LD no. 1559496(SEQ ID NO:505), Ceres CLONE ID no. 530984 (SEQ ID NO:507), Public GI IDno. 61611682 (SEQ ID NO:509), Public GI ID no. 36789785 (SEQ ID NO:512),Ceres CLONE ID no. 702632 (SEQ ID NO:514), Public GI LD no. 61657299(SEQ LD NO:515), Public GI ID no. 10946337 (SEQ ID NO:516), Ceres CLONEID no. 1996408 (SEQ ID NO:518), Ceres CLONE ID no. 1725313 (SEQ IDNO:520), Public GI LD no. 78058606 (SEQ ID NO:521), Public GI ID no.125538317 (SEQ ID NO:522), Public GI ID no. 125556324 (SEQ ID NO:523),Public GI ID no. 125548890 (SEQ ID NO:524), Public GI ID no. 93211100(SEQ ID NO:525), Public GI ID no. 115444217 (SEQ ID NO:526), Public GIID no. 115467558 (SEQ ID NO:527), Public GI ID no. 11094209 (SEQ IDNO:528), Public GI LD no. 125596830 (SEQ ID NO:529), Public GI ID no.115469296 (SEQ ID NO:530), Public GI ID no. 115447239 (SEQ ID NO:531),Public GI ID no. 21655154 (SEQ ID NO:532), Public GI ID no. 21667485(SEQ ID NO:533), Public GI ID no. 21667475 (SEQ ID NO:534), Public GI LDno. 21655158 (SEQ ID NO:535), and sequences identified as functionalhomologs of the sequences of FIG. 6, as set forth in the sequencelisting.

Polypeptides are shown in the sequence listing that have HMM bit scoresgreater than 20 when fitted to an HMM generated from the amino acidsequences set forth in FIG. 7. Such polypeptides include At1g70270 (SEQID NO:634), Public GI ID no. 98961985 (SEQ ID NO:637), Ceres CLONE IDno. 1916112 (SEQ ID NO:636), Public GI ID no. 9369405 (SEQ ID NO:638),Public GI ID no. 9369406 (SEQ ID NO:639), Ceres CLONE ID no. 1238706(SEQ ID NO:641), and sequences identified as functional homologs of thesequences of FIG. 7, as set forth in the sequence listing.

Polypeptides are shown in the sequence listing that have HMM bit scoresgreater than 80 when fitted to an HMM generated from the amino acidsequences set forth in FIG. 8. Such polypeptides include At4g25480 (SEQID NO:644), SEQ ID NO:645, Ceres CLONE ID no. 1849479 (SEQ ID NO:767),Public GI ID no. 89275008 (SEQ ID NO:796), Public GI ID no. 120400525(SEQ ID NO:797), Public GI ID no. 98980426 (SEQ ID NO:804), Public GI IDno. 71983373 (SEQ ID NO:808). Public GI ID no. 41351817 (SEQ ID NO:809),Public GI ID no. 76446191 (SEQ ID NO:811), Public GI ID no. 5616086 (SEQID NO:813), Ceres CLONE ID no. 1052602 (SEQ ID NO:826), Public GI ID no.72068957 (SEQ ID NO:830), Public GI ID no. 71534113 (SEQ ID NO:831),Public GI ID no. 37147896 (SEQ ID NO:832), Public GI ID no. 92918850(SEQ ID NO:834), Public GI ID no. 40647095 (SEQ ID NO:835), Ceres ANNOTID no. 1527711 (SEQ ID NO:837), Public GI ID no. 71041116 (SEQ IDNO:838), Public GI ID no. 12003384 (SEQ ID NO:839), Public GI ID no.18535580 (SEQ ID NO:840), Ceres CLONE ID no. 991178 (SEQ ID NO:647),Ceres CLONE ID no. 1626038 (SEQ ID NO:649), Ceres CLONE ID no. 341615(SEQ ID NO:651), Ceres CLONE ID no. 1832518 (SEQ ID NO:653), Ceres CLONEID no. 1832588 (SEQ ID NO:655), Ceres CLONE ID no. 1936806 (SEQ IDNO:657), Ceres CLONE ID no. 973892 (SEQ ID NO:659), Ceres CLONE ID no.565251 (SEQ ID NO:661), Ceres CLONE ID no. 681088 (SEQ ID NO:663), CeresCLONE ID no. 707775 (SEQ ID NO:665), Ceres CLONE ID no. 453357 (SEQ IDNO:667). Ceres CLONE ID no. 1916958 (SEQ ID NO:669), Ceres CLONE ID no.1940632 (SEQ ID NO:671), Ceres CLONE ID no. 476784 (SEQ ID NO:673),Ceres CLONE ID no. 1869284 (SEQ ID NO:675), Public GI ID no. 125540662(SEQ ID NO:676), Ceres CLONE ID no. 1648272 (SEQ ID NO:678), Ceres CLONEID no. 1987804 (SEQ ID NO:680), Ceres CLONE ID no. 1675695 (SEQ IDNO:682), Ceres CLONE ID no. 1169111 (SEQ ID NO:684), Ceres CLONE ID no.572121 (SEQ ID NO:686), Ceres CLONE ID no. 1674836 (SEQ ID NO:688),Ceres ANNOT ID no. 1486207 (SEQ ID NO:690), Ceres CLONE ID no. 2023610(SEQ ID NO:692), Ceres ANNOT ID no. 1496976 (SEQ ID NO:694), Public GIID no. 116310031 (SEQ TD NO:695), Ceres CLONE ID no. 1626363 (SEQ IDNO:697), Ceres ANNOT ID no. 1483747 (SEQ ID NO:699), Ceres ANNOT ID no.1471330 (SEQ ID NO:701), Ceres CLONE ID no. 101144964 (SEQ ID NO:702),Ceres ANNOT ID no. 1439439 (SEQ ID NO:704), Ceres CLONE ID no. 1446565(SEQ ID NO:706), Ceres CLONE ID no. 1951962 (SEQ ID NO:708), Ceres CLONEID no. 100960656 (SEQ ID NO:709), Ceres CLONE ID no. 285154 (SEQ IDNO:711), Public GI ID no. 61968916 (SEQ ID NO:712), Public GI ID no.118026854 (SEQ ID NO:713), Public GI ID no. 63098612 (SEQ ID NO:714),Ceres ANNOT ID no. 1522310 (SEQ ID NO:716), Ceres CLONE ID no. 1854375(SEQ ID NO:718), Ceres CLONE ID no. 709819 (SEQ ID NO:720), Public GI IDno. 115447695 (SEQ ID NO:721), Ceres CLONE ID no. 1726356 (SEQ IDNO:723), Ceres CLONE ID no. 1762419 (SEQ ID NO:725), Public GI ID no.63098606 (SEQ ID NO:726), Ceres CLONE ID no. 1766572 (SEQ ID NO:728),Ceres CLONE ID no. 281871 (SEQ ID NO:730), Ceres CLONE ID no. 1560970(SEQ ID NO:732), Ceres CLONE ID no. 1760747 (SEQ ID NO:734), Ceres ANNOTID no. 1438772 (SEQ ID NO:736), Ceres ANNOT ID no. 1447378 (SEQ IDNO:738), Ceres ANNOT ID no. 1453360 (SEQ ID NO:740), Public GI ID no.33637698 (SEQ ID NO:741), Public GI ID no. 118026860 (SEQ ID NO:742),Public GI ID no. 60116232 (SEQ ID NO:743), Public GI ID no. 115477639(SEQ ID NO:744), Public GI ID no. 126567023 (SEQ ID NO:745), Ceres CLONEID no. 988971 (SEQ ID NO:747), Ceres CLONE ID no. 1464521 (SEQ IDNO:749), Public GI ID no. 63098610 (SEQ ID NO:750), Public GI ID no.126566972 (SEQ ID NO:751), Ceres CLONE ID no. 1556129 (SEQ ID NO:753),Ceres CLONE ID no. 1761385 (SEQ ID NO:755), Ceres ANNOT ID no. 1488325(SEQ ID NO:757), Ceres ANNOT ID no. 1460483 (SEQ ID NO:759), Ceres CLONEID no. 1837825 (SEQ ID NO:761), Public GI ID no. 27228310 (SEQ IDNO:762), Public GI ID no. 117653881 (SEQ ID NO:763), Public GI ID no.115480233 (SEQ ID NO:764), Public GI ID no. 37694048 (SEQ ID NO:765),Ceres CLONE ID no. 1934653 (SEQ ID NO:769), Ceres CLONE ID no. 1608106(SEQ ID NO:771), Ceres CLONE ID no. 1604576 (SEQ ID NO:773), Public GIID no. 55824656 (SEQ ID NO:774), Ceres CLONE ID no. 1620272 (SEQ IDNO:776), Ceres CLONE ID no. 1853170 (SEQ ID NO:778), Public GI ID no.79013962 (SEQ ID NO:779), Public GI ID no. 98975385 (SEQ ID NO:780),Ceres ANNOT ID no. 1438775 (SEQ ID NO:782), Public GI ID no. 23495460(SEQ ID NO:783), Public GI ID no. 98975377 (SEQ ID NO:784), Ceres ANNOTID no. 1438776 (SEQ ID NO:786), Ceres CLONE ID no. 1853601 (SEQ IDNO:788), Ceres CLONE ID no. 1609048 (SEQ ID NO:790), Ceres CLONE ID no.322305 (SEQ ID NO:792), Ceres CLONE ID no. 1823713 (SEQ ID NO:794),Public GI ID no. 3660548 (SEQ ID NO:795), Public GI ID no. 56154991 (SEQTD NO:798), Public GI ID no. 2980802 (SEQ ID NO:799), Public GI ID no.7269398 (SEQ ID NO:800), Public GI ID no. 18416557 (SEQ ID NO:801),Public GI ID no. 56154992 (SEQ ID NO:802), Public GI ID no. 4091984 (SEQID NO:803), Public GI ID no. 1899058 (SEQ ID NO:805), Public GI ID no.56154990 (SEQ ID NO:806), Public GI ID no. 18416562 (SEQ ID NO:807),Public GI ID no. 38683266 (SEQ ID NO:810), Public GI ID no. 39983638(SEQ ID NO:812), Public GI ID no. 38426954 (SEQ ID NO:814), Public GI IDno. 38426948 (SEQ ID NO:815), Public GI ID no. 38146944 (SEQ ID NO:816),Public GI ID no. 38426952 (SEQ ID NO:817), Public GI ID no. 20303011(SEQ ID NO:818), Public GI ID no. 66269982 (SEQ ID NO:819). Public GI IDno. 89212816 (SEQ ID NO:820), Public GI ID no. 20303015 (SEQ ID NO:821),Public GI ID no. 38426950 (SEQ ID NO:822), Public GI ID no. 15242244(SEQ ID NO:823), Public GI ID no. 116831599 (SEQ ID NO:824), Public GIID no. 66269671 (SEQ ID NO:827), Ceres ANNOT ID no. 1468919 (SEQ IDNO:829), Public GI ID no. 57903606 (SEQ ID NO:833), Public GI ID no.45826358 (SEQ ID NO:841), Ceres ANNOT ID no. 6085912 (SEQ ID NO:843),Ceres ANNOT ID no. 6026171 (SEQ ID NO:845), Ceres ANNOT ID no. 6031706(SEQ ID NO:847), Public GI ID no. 115353971 (SEQ ID NO:1843), andsequences identified as functional homologs of the sequences of FIG. 8,as set forth in the sequence listing.

Polypeptides are shown in the sequence listing that have HMM bit scoresgreater than 170 when fitted to an HMM generated from the amino acidsequences set forth in FIG. 9. Such polypeptides include A2g33780 (SEQID NO:850), Ceres CLONE ID no. 1833093 (SEQ ID NO:853), Ceres ANNOT IDno. 1502190 (SEQ ID NO:857), Ceres CLONE ID no. 565641 (SEQ ID NO:876),Public GI ID no. 87240507 (SEQ ID NO:877), Ceres CLONE ID no. 1325382(SEQ ID NO:881), Ceres CLONE ID no. 1558265 (SEQ ID NO:885), Ceres CLONEID no. 1823669 (SEQ ID NO:895), Public GI ID no. 115464921 (SEQ IDNO:898), Ceres CLONE ID no. 100040598 (SEQ ID NO:851), Ceres CLONE IDno. 1847967 (SEQ ID NO:855), Ceres ANNOT ID no. 1449186 (SEQ ID NO:859),Ceres ANNOT ID no. 1466723 (SEQ ID NO:861), Public GI ID no. 21805688(SEQ ID NO:862), Public GI ID no. 9795609 (SEQ ID NO:863), Public GI IDno. 13877535 (SEQ ID NO:864), Public GI ID no. 15232547 (SEQ ID NO:865),Public GI ID no. 15238851 (SEQ ID NO:866), Ceres CLONE ID no. 123863(SEQ ID NO:868), Ceres CLONE ID no. 652496 (SEQ ID NO:870), Ceres CLONEID no. 1656707 (SEQ ID NO:872), Ceres CLONE ID no. 1660346 (SEQ IDNO:874), Ceres CLONE ID no. 678878 (SEQ ID NO:879), Ceres CLONE ID no.340102 (SEQ ID NO:883), Ceres CLONE ID no. 330491 (SEQ ID NO:887), CeresCLONE ID no. 992304 (SEQ ID NO:889), Ceres CLONE ID no. 1509925 (SEQ IDNO:891), Ceres CLONE ID no. 1543852 (SEQ ID NO:893), Ceres CLONE ID no.1785736 (SEQ ID NO:897), Ceres ANNOT ID no. 6079909 (SEQ ID NO:900),Ceres ANNOT ID no. 6040353 (SEQ ID NO:902), Ceres ANNOT ID no. 6100173(SEQ ID NO:904), and sequences identified as functional homologs of thesequences of FIG. 9, as set forth in the sequence listing.

Polypeptides are shown in the sequence listing that have HMM bit scoresgreater than 80 when fitted to an HMM generated from the amino acidsequences set forth in FIG. 10. Such polypeptides include At4g17810 (SEQID NO:907), Ceres CLONE ID no. 1940797 (SEQ ID NO:909), Ceres ANNOT IDno. 1538900 (SEQ ID NO:911), Ceres CLONE ID no. 1126868 (SEQ ID NO:922),Public GI ID no. 89257684 (SEQ ID NO:923), Public GI ID no. 124360460(SEQ ID NO:929), Public GI ID no. 62865694 (SEQ ID NO:931), Public GI IDno. 62865692 (SEQ ID NO:932), Ceres CLONE ID no. 260368 (SEQ ID NO:936),Ceres CLONE ID no. 1873510 (SEQ ID NO:947), Public GI ID no. 125541662(SEQ ID NO:948), Public GI ID no. 48716268 (SEQ ID NO:950), Ceres ANNOTID no. 1529131 (SEQ ID NO:913), Ceres ANNOT ID no. 1454060 (SEQ IDNO:915), Ceres ANNOT ID no. 1442787 (SEQ ID NO:917), Ceres ANNOT ID no.1452648 (SEQ ID NO:919), Public GI ID no. 2245140 (SEQ ID NO:920),Public GI ID no. 89274212 (SEQ ID NO:924), Ceres CLONE ID no. 1104523(SEQ ID NO:926), Ceres CLONE ID no. 654265 (SEQ ID NO:928), Public GI IDno. 42627704 (SEQ ID NO:930), Ceres CLONE ID no. 887222 (SEQ ID NO:934),Public GI ID no. 62865690 (SEQ ID NO:937), Public GI ID no. 64175600(SEQ ID NO:938), Public GI ID no. 64175634 (SEQ ID NO:939), Public GI IDno. 64175606 (SEQ ID NO:940), Public GI ID no. 64175648 (SEQ ID NO:941),Ceres CLONE ID no. 312184 (SEQ ID NO:943), Ceres CLONE ID no. 380740(SEQ ID NO:945), Public GI ID no. 125531536 (SEQ ID NO:949), Public GIID no. 62865696 (SEQ ID NO:1844), and sequences identified as functionalhomologs of the sequences of FIG. 10, as set forth in the sequencelisting.

Polypeptides are shown in the sequence listing that have HMM bit scoresgreater than 60 when fitted to an HMM generated from the amino acidsequences set forth in FIG. 11. Such polypeptides include At1g13360 (SEQID NO:951), Ceres CLONE ID no. 1798705 (SEQ ID NO:955), Ceres ANNOT IDno. 1458907 (SEQ ID NO:963). Ceres CLONE ID no. 1090409 (SEQ ID NO:971).Ceres CLONE ID no. 479817 (SEQ ID NO:977), Ceres CLONE ID no. 1041793(SEQ ID NO:979), Ceres CLONE ID no. 684633 (SEQ ID NO:985), Ceres CLONEID no. 371815 (SEQ ID NO:991), Ceres CLONE ID no. 1686460 (SEQ IDNO:993), Ceres CLONE ID no. 1448595 (SEQ ID NO:995), Ceres CLONE ID no.1734477 (SEQ ID NO:999), Ceres CLONE ID no. 1605693 (SEQ ID NO:1005),Ceres CLONE ID no. 1757400 (SEQ ID NO:1009), Public GI ID no. 115434334(SEQ ID NO:1015), Ceres CLONE ID no. 1793754 (SEQ ID NO:957), CeresCLONE ID no. 1938045 (SEQ ID NO:959), Ceres CLONE ID no. 1850004 (SEQ IDNO:961), Ceres ANNOT ID no. 1489548 (SEQ ID NO:965), Public GI ID no.22329538 (SEQ ID NO:966), Public GI ID no. 18404714 (SEQ ID NO:967),Ceres CLONE ID no. 1110032 (SEQ ID NO:969), Ceres CLONE ID no. 1095353(SEQ ID NO:973), Ceres CLONE ID no. 872121 (SEQ ID NO:975), Ceres CLONEID no. 562208 (SEQ ID NO:981), Ceres CLONE ID no. 1042364 (SEQ IDNO:983), Ceres CLONE ID no. 1031873 (SEQ ID NO:987), Ceres CLONE ID no.1377698 (SEQ ID NO:989), Ceres CLONE ID no. 1742945 (SEQ ID NO:997),Ceres CLONE ID no. 1742053 (SEQ ID NO:1001), Ceres CLONE ID no. 1728365(SEQ ID NO:1003), Ceres CLONE ID no. 1609807 (SEQ ID NO:1007), CeresCLONE ID no. 1778566 (SEQ ID NO:1011), Ceres CLONE ID no. 2020580 (SEQID NO:1013), Public GI ID no. 125524285 (SEQ ID NO:1014), Public GI IDno. 125568898 (SEQ ID NO:1016), Ceres ANNOT ID no. 6055303 (SEQ IDNO:1018), and sequences identified as functional homologs of thesequences of FIG. 11, as set forth in the sequence listing.

Polypeptides are shown in the sequence listing that have HMM bit scoresgreater than 140 when fitted to an HMM generated from the amino acidsequences set forth in FIG. 12. Such polypeptides include At1g75860 (SEQID NO:1024), Ceres ANNOT ID no. 1452905 (SEQ ID NO:1029), Ceres CLONE IDno. 956176 (SEQ ID NO:1039), Public GI ID no. 92870366 (SEQ ID NO:1040),Ceres CLONE ID no. 294166 (SEQ ID NO:1042), Public GI ID no. 125543067(SEQ ID NO:1043), SEQ ID NO:1025, Ceres ANNOT ID no. 1442522 (SEQ IDNO:1027), Public GI TD no. 8778818 (SEQ ID NO:1030), Ceres CLONE ID no.108095 (SEQ ID NO:1032), Public GI ID no. 18394821 (SEQ ID NO:1033),Ceres CLONE ID no. 6332 (SEQ ID NO:1035), Ceres CLONE ID no. 1069047(SEQ ID NO:1037), Public GI ID no. 115480956 (SEQ ID NO:1044), andsequences identified as functional homologs of the sequences of FIG. 12,as set forth in the sequence listing.

Polypeptides are shown in the sequence listing that have HMM bit scoresgreater than 80 when fitted to an HMM generated from the amino acidsequences set forth in FIG. 13. Such polypeptides include At4g19700 (SEQID NO:1047), Ceres CLONE ID no. 1837694 (SEQ ID NO:1053), Ceres ANNOT IDno. 1483367 (SEQ ID NO:1057), Ceres CLONE ID no. 1077781 (SEQ IDNO:1083), Ceres CLONE ID no. 471026 (SEQ ID NO:1085), Public GI ID no.92888885 (SEQ ID NO:1099), Public GI ID no. 45544873 (SEQ ID NO:1100),Public GI ID no. 45758663 (SEQ ID NO:1101). Ceres CLONE ID no. 772927(SEQ ID NO: 1105), Ceres CLONE ID no. 895080 (SEQ ID NO:1111), CeresCLONE ID no. 1806128 (SEQ ID NO:1131), Public GI ID no. 115458192 (SEQID NO:1134), Public GI ID no. 82470795 (SEQ ID NO: 1139), Ceres CLONE IDno. 1837746 (SEQ ID NO:1049), Ceres CLONE ID no. 1834764 (SEQ IDNO:1051), Ceres CLONE ID no. 1853547 (SEQ ID NO:1055), Ceres ANNOT IDno. 1474088 (SEQ ID NO:1059), Ceres ANNOT ID no. 1536919 (SEQ IDNO:1061), Ceres ANNOT ID no. 1467033 (SEQ ID NO:1063), Ceres ANNOT IDno. 1485401 (SEQ ID NO:1065), Ceres ANNOT ID no. 1486505 (SEQ IDNO:1067). Public GI ID no. 17065054 (SEQ ID NO:1068), Public GI ID no.30694690 (SEQ ID NO:1069), Ceres CLONE ID no. 12997 (SEQ ID NO:1071),Public GI ID no. 30694694 (SEQ ID NO:1072). Public GI ID no. 42572167(SEQ ID NO:1073), Public GI ID no. 110739742 (SEQ ID NO:1074), Public GIID no. 18412263 (SEQ ID NO:1075), Ceres CLONE ID no. 36412 (SEQ IDNO:1077), Public GI ID no. 18399792 (SEQ ID NO:1078), Ceres CLONE ID no.924 (SEQ ID NO:1080), Public GI ID no. 15238000 (SEQ ID NO:1081), CeresCLONE ID no. 1626330 (SEQ ID NO:1087), Ceres CLONE ID no. 1650419 (SEQID NO:1089), Ceres CLONE ID no. 1641329 (SEQ ID NO:1091), Ceres CLONE IDno. 1620406 (SEQ ID NO:1093), Ceres CLONE ID no. 546832 (SEQ IDNO:1095), Ceres CLONE ID no. 1243138 (SEQ ID NO:1097), Public GI ID no.92887260 (SEQ ID NO:1098), Ceres CLONE ID no. 885628 (SEQ ID NO: 1103),Ceres CLONE ID no. 1376391 (SEQ ID NO: 1107). Ceres CLONE ID no. 465893(SEQ ID NO: 1109). Ceres CLONE ID no. 218243 (SEQ ID NO:1113), CeresCLONE ID no. 1558456 (SEQ ID NO: 1115), Ceres CLONE ID no. 343008 (SEQID NO: 1117), Ceres CLONE ID no. 218463 (SEQ ID NO: 1119), Ceres CLONEID no. 1565409 (SEQ ID NO:1121), Ceres CLONE ID no. 1060968 (SEQ ID NO:1123), Ceres CLONE ID no. 236111 (SEQ ID NO: 1125), Ceres CLONE ID no.285598 (SEQ ID NO:1127), Ceres CLONE ID no. 225881 (SEQ ID NO:1129),Ceres CLONE ID no. 1811383 (SEQ ID NO:1133), Public GI ID no. 49388268(SEQ ID NO:1135), Public GI ID no. 125590268 (SEQ ID NO: 1136), PublicGI ID no. 115444009 (SEQ ID NO:1137), Public GI ID no. 115447993 (SEQ IDNO: 1138), Ceres ANNOT ID no. 6033842 (SEQ ID NO:1141), Ceres ANNOT IDno. 6029952 (SEQ ID NO:1143), Ceres ANNOT ID no. 6035837 (SEQ IDNO:1145). Ceres ANNOT ID no. 6035830 (SEQ ID NO:1147), Ceres ANNOT IDno. 6029981 (SEQ ID NO:1149), and sequences identified as functionalhomologs of the sequences of FIG. 13, as set forth in the sequencelisting.

Polypeptides are shown in the sequence listing that have HMM bit scoresgreater than 80 when fitted to an HMM generated from the amino acidsequences set forth in FIG. 14. Such polypeptides include At1g58100 (SEQID NO:1151), Ceres CLONE ID no. 1851526 (SEQ ID NO: 1155), Ceres ANNOTID no. 1486769 (SEQ ID NO:1172), Public GI ID no. 83032232 (SEQ IDNO:1209), Ceres CLONE ID no. 1620420 (SEQ ID NO:1211), Public GI ID no.92892428 (SEQ ID NO:1215), Ceres CLONE ID no. 884742 (SEQ ID NO:1223),Ceres CLONE ID no. 1821559 (SEQ ID NO:1246), Public GI ID no. 51535021(SEQ ID NO:1258), Public GI ID no. 113205304 (SEQ ID NO:1263), Public GIID no. 37719051 (SEQ ID NO:1264), Ceres CLONE ID no. 1918070 (SEQ ID NO:1153), Ceres CLONE ID no. 1948426 (SEQ ID NO:1157), Ceres CLONE ID no.1937875 (SEQ ID NO: 1159), Ceres CLONE ID no. 100056542 (SEQ ID NO:1160), Public GI ID no. 5731257 (SEQ ID NO:1161), Ceres CLONE ID no.100058043 (SEQ ID NO: 1162), Ceres CLONE ID no. 1838288 (SEQ ID NO:1164), Ceres CLONE ID no. 1793597 (SEQ ID NO: 1166), Ceres ANNOT ID no.1543031 (SEQ ID NO: 1168), Ceres ANNOT ID no. 1489643 (SEQ ID NO: 1170),Ceres ANNOT ID no. 1479721 (SEQ ID NO: 1174), Ceres ANNOT ID no. 1449170(SEQ ID NO: 1176), Ceres ANNOT ID no. 1493696 (SEQ ID NO:1178), CeresANNOT ID no. 1543534 (SEQ ID NO:1180), Ceres ANNOT ID no. 1440815 (SEQID NO: 1182), Ceres ANNOT ID no. 1490137 (SEQ ID NO: 1184). Ceres ANNOTID no. 1451054 (SEQ ID NO: 1186), Ceres ANNOT ID no. 1456669 (SEQ IDNO:1188), Ceres ANNOT ID no. 1509865 (SEQ ID NO: 1190), Ceres ANNOT IDno. 1447910 (SEQ ID NO: 1192), Ceres ANNOT ID no. 1471068 (SEQ IDNO:1194), Ceres ANNOT ID no. 1504118 (SEQ ID NO:1196), Ceres CLONE IDno. 1343621 (SEQ ID NO:1198), Public GI ID no. 15218305 (SEQ IDNO:1199), Public GI ID no. 15219640 (SEQ ID NO:1200), Public GI ID no.18409345 (SEQ ID NO:1201), Public GI ID no. 6522545 (SEQ ID NO:1202),Public GI ID no. 15237274 (SEQ ID NO:1203), Public GI ID no. 26452377(SEQ ID NO:1204), Ceres CLONE ID no. 33629 (SEQ ID NO:1206), Ceres CLONEID no. 1064407 (SEQ ID NO:1208), Ceres CLONE ID no. 1656310 (SEQ IDNO:1213), Public GI ID no. 92885257 (SEQ ID NO:1214), Public GI ID no.92868571 (SEQ ID NO:1216), Public GI ID no. 53689778 (SEQ ID NO:1217).Ceres CLONE ID no. 835598 (SEQ ID NO:1219), Ceres CLONE ID no. 575649(SEQ ID NO:1221), Ceres CLONE ID no. 376567 (SEQ ID NO:1225), CeresCLONE ID no. 1284191 (SEQ ID NO:1227), Ceres CLONE ID no. 367175 (SEQ IDNO:1229), Ceres CLONE ID no. 100748296 (SEQ ID NO:1230), Ceres CLONE IDno. 1597176 (SEQ ID NO:1232), Ceres CLONE ID no. 375636 (SEQ IDNO:1234), Ceres CLONE ID no. 288123 (SEQ ID NO:1236), Ceres CLONE ID no.303582 (SEQ ID NO:1238), Ceres CLONE ID no. 1604759 (SEQ ID NO:1240),Ceres CLONE ID no. 1955192 (SEQ ID NO:1242), Ceres CLONE ID no. 2008687(SEQ ID NO:1244), Ceres CLONE ID no. 1995843 (SEQ ID NO:1248), CeresCLONE ID no. 2008591 (SEQ ID NO:1250), Ceres CLONE ID no. 2046826 (SEQID NO:1252), Ceres CLONE ID no. 1985573 (SEQ ID NO:1254), Public GI IDno. 125541129 (SEQ ID NO:1255), Public GI ID no. 125528922 (SEQ IDNO:1256), Public GI ID no. 115487590 (SEQ ID NO:1257), Public GI ID no.115448671 (SEQ ID NO:1259), Public GI ID no. 125596564 (SEQ ID NO:1260),Public GI ID no. 125573161 (SEQ ID NO:1261). Public GI ID no. 48716463(SEQ ID NO:1262), Ceres ANNOT ID no. 6054246 (SEQ ID NO:1266), CeresANNOT ID no. 6086570 (SEQ ID NO:1268), Ceres ANNOT ID no. 6024957 (SEQID NO:1270), Ceres ANNOT ID no. 6016867 (SEQ ID NO:1272), Ceres ANNOT IDno. 6091369 (SEQ ID NO:1274), and sequences identified as functionalhomologs of the sequences of FIG. 14, as set forth in the sequencelisting.

Polypeptides are shown in the sequence listing that have HMM bit scoresgreater than 180 when fitted to an HMM generated from the amino acidsequences set forth in FIG. 15. Such polypeptides include At5g46170 (SEQID NO:1277), Ceres CLONE ID no. 1926352 (SEQ ID NO:1279), Ceres ANNOT IDno. 1448905 (SEQ ID NO:1285). Public GI ID no. 15236865 (SEQ IDNO:1294). Ceres CLONE ID no. 934771 (SEQ ID NO:1301), Ceres CLONE ID no.338386 (SEQ ID NO:1303), Ceres CLONE ID no. 1780691 (SEQ ID NO:1317),Public GI ID no. 115464819 (SEQ ID NO:1326), Ceres CLONE ID no. 1848576(SEQ ID NO:1281), Ceres CLONE ID no. 1981528 (SEQ ID NO:1283), CeresANNOT ID no. 1465978 (SEQ ID NO:1287). Ceres ANNOT ID no. 1504997 (SEQID NO:1289), Ceres ANNOT ID no. 1451909 (SEQ ID NO:1291), Ceres ANNOT IDno. 1461635 (SEQ ID NO:1293), Public GI ID no. 18397400 (SEQ IDNO:1295), Ceres CLONE ID no. 16226 (SEQ ID NO:1297), Public GI ID no.18411823 (SEQ ID NO:1298), Public GI ID no. 15219845 (SEQ TD NO:1299),Ceres CLONE ID no. 1276710 (SEQ ID NO:1305), Ceres CLONE ID no. 1479310(SEQ ID NO:1307), Ceres CLONE ID no. 376230 (SEQ ID NO:1309), CeresCLONE ID no. 1290713 (SEQ ID NO:1311), Ceres CLONE ID no. 321681 (SEQ IDNO:1313), Ceres CLONE ID no. 1869072 (SEQ ID NO:1315), Ceres CLONE IDno. 1818502 (SEQ ID NO:1319), Ceres CLONE ID no. 1750477 (SEQ IDNO:1321). Public GI ID no. 125552947 (SEQ ID NO:1322), Public GI ID no.125527862 (SEQ ID NO:1323), Public GI ID no. 125543660 (SEQ ID NO:1324),Public GI ID no. 125528123 (SEQ ID NO:1325), Public GI ID no. 115440195(SEQ ID NO:1327), Public GI ID no. 115452717 (SEQ ID NO:1328), Public GIID no. 115440629 (SEQ ID NO:1329). Public GI ID no. 115464599 (SEQ IDNO:1330), Public GI ID no. 20161462 (SEQ ID NO:1331), Public GI ID no.125586076 (SEQ ID NO:1332), Ceres CLONE ID no. 1823216 (SEQ ID NO:1334),Ceres ANNOT ID no. 6040230 (SEQ ID NO:1336), Ceres ANNOT ID no. 6015489(SEQ ID NO:1338), Ceres ANNOT ID no. 6042890 (SEQ ID NO:1340), CeresANNOT ID no. 6040033 (SEQ ID NO:1342), Ceres ANNOT ID no. 6018414 (SEQID NO:1344), and sequences identified as functional homologs of thesequences of FIG. 15, as set forth in the sequence listing.

Polypeptides are shown in the sequence listing that have HMM bit scoresgreater than 60 when fitted to an HMM generated from the amino acidsequences set forth in FIG. 16. Such polypeptides include At4g32280 (SEQID NO:1347), Ceres CLONE ID no. 285028 (SEQ ID NO:1419), Ceres CLONE IDno. 100969565 (SEQ ID NO:1422), Public GI ID no. 1352057 (SEQ IDNO:1427), Ceres ANNOT ID no. 1453784 (SEQ ID NO:1429), Public GI ID no.452777 (SEQ ID NO:1430), Public GI ID no. 92873297 (SEQ ID NO:1431),Ceres ANNOT ID no. 1452612 (SEQ ID NO:1349), Ceres CLONE ID no. 520455(SEQ ID NO:1351), Public GI TD no. 75271810 (SEQ ID NO:1352), Public GIID no. 115489446 (SEQ ID NO:1353), Ceres CLONE ID no. 499878 (SEQ IDNO:1355), Ceres ANNOT ID no. 1491840 (SEQ ID NO:1357), Public GI ID no.125587204 (SEQ ID NO:1358), Ceres CLONE ID no. 320997 (SEQ ID NO:1360),Ceres ANNOT ID no. 1455585 (SEQ ID NO:1362), Ceres ANNOT ID no. 1499460(SEQ ID NO:1364), Ceres CLONE ID no. 334484 (SEQ ID NO:1366), CeresCLONE ID no. 100819481 (SEQ ID NO:1367). Public GI ID no. 115462401 (SEQID NO:1368), Ceres CLONE ID no. 1448136 (SEQ ID NO:1370), Ceres CLONE IDno. 277751 (SEQ ID NO:1372), Ceres ANNOT ID no. 1491839 (SEQ IDNO:1374), Ceres CLONE ID no. 100913241 (SEQ ID NO:1375), Ceres CLONE IDno. 1053224 (SEQ ID NO:1377), Ceres CLONE ID no. 425766 (SEQ IDNO:1379), Ceres CLONE ID no. 485480 (SEQ ID NO:1381), Ceres CLONE ID no.474845 (SEQ ID NO:1383), Ceres CLONE ID no. 354561 (SEQ ID NO:1385),Ceres CLONE ID no. 540858 (SEQ ID NO:1387), Ceres CLONE ID no. 2032994(SEQ ID NO:1389), Ceres CLONE ID no. 2015315 (SEQ ID NO:1391), CeresCLONE ID no. 2016149 (SEQ ID NO:1393), Ceres CLONE ID no. 1922843 (SEQID NO:1395), Ceres CLONE ID no. 2000263 (SEQ ID NO:1397), Ceres CLONE IDno. 1943510 (SEQ ID NO:1399), Ceres CLONE ID no. 1835498 (SEQ IDNO:1401), Ceres CLONE ID no. 101116694 (SEQ ID NO:1402), Ceres CLONE IDno. 1930596 (SEQ ID NO:1404), Ceres CLONE ID no. 846036 (SEQ IDNO:1406), Ceres CLONE ID no. 941614 (SEQ ID NO:1408), Ceres CLONE ID no.238788 (SEQ ID NO:1410), Public GI ID no. 125554220 (SEQ ID NO:1411),Public GI ID no. 125559895 (SEQ ID NO:1412), Public GI ID no. 75252070(SEQ ID NO:1413), Public GI ID no. 115466632 (SEQ ID NO:1414), Public GIID no. 125541525 (SEQ ID NO:1415), Ceres CLONE ID no. 1805110 (SEQ IDNO:1417), Ceres CLONE ID no. 1725309 (SEQ ID NO:1421), Ceres CLONE IDno. 100861679 (SEQ ID NO:1423), Public GI ID no. 75226278 (SEQ IDNO:1424), Public GI ID no. 125525030 (SEQ ID NO:1425). Public GI ID no.115435474 (SEQ ID NO:1426), Ceres CLONE ID no. 1728516 (SEQ ID NO:1433),Public GI ID no. 115467910 (SEQ ID NO:1434), Public GI ID no. 15239950(SEQ ID NO:1435), Public GI ID no. 4887012 (SEQ ID NO:1436), Ceres ANNOTID no. 1478544 (SEQ ID NO:1438), Public GI ID no. 90811713 (SEQ IDNO:1439), Public GI ID no. 25989504 (SEQ ID NO:1440), Ceres CLONE ID no.1113354 (SEQ ID NO:1442), Ceres CLONE ID no. 1113630 (SEQ ID NO:1444),Ceres ANNOT ID no. 6072030 (SEQ ID NO:1446). Ceres ANNOT ID no. 6025654(SEQ ID NO:1448), Ceres ANNOT ID no. 6091150 (SEQ ID NO:1450), CeresANNOT ID no. 6100390 (SEQ ID NO:1452), and sequences identified asfunctional homologs of the sequences of FIG. 16, as set forth in thesequence listing.

Polypeptides are shown in the sequence listing that have HMM bit scoresgreater than 270 when fitted to an HMM generated from the amino acidsequences set forth in FIG. 17. Such polypeptides include At3g02830 (SEQID NO:1457), Ceres CLONE ID no. 1924904 (SEQ ID NO:1460), Ceres ANNOT IDno. 1543346 (SEQ ID NO:1462). Public GI ID no. 18396338 (SEQ IDNO:1467), Ceres CLONE ID no. 833872 (SEQ ID NO:1471), Ceres CLONE ID no.1579587 (SEQ ID NO:1475), Ceres CLONE ID no. 1786411 (SEQ ID NO:1477),Public GI ID no. 108864370 (SEQ ID NO:1480), SEQ ID NO:1458, Ceres ANNOTID no. 1532932 (SEQ ID NO:1464), Ceres ANNOT ID no. 1489955 (SEQ IDNO:1466), Public GI ID no. 4928917 (SEQ ID NO:1468), Public GI ID no.6728979 (SEQ ID NO:1469), Ceres CLONE ID no. 285780 (SEQ ID NO:1473),Public GI ID no. 125528863 (SEQ ID NO:1478), Public GI ID no. 125536365(SEQ ID NO:1479), Public GI ID no. 108864369 (SEQ ID NO:1481), Public GIID no. 115488274 (SEQ ID NO:1482), Public GI ID no. 125577099 (SEQ IDNO:1483), Public GI ID no. 125573110 (SEQ ID NO:1484), Public GI ID no.124359159 (SEQ ID NO:1485), Public GI ID no. 62901479 (SEQ ID NO:1486),Ceres ANNOT ID no. 6016783 (SEQ ID NO:1488), Ceres ANNOT ID no. 6020759(SEQ ID NO:1490), Ceres ANNOT ID no. 6028676 (SEQ ID NO:1492). CeresANNOT ID no. 6028677 (SEQ ID NO:1494), and sequences identified asfunctional homologs of the sequences of FIG. 17, as set forth in thesequence listing.

Polypeptides are shown in the sequence listing that have HMM bit scoresgreater than 70 when fitted to an HMM generated from the amino acidsequences set forth in FIG. 18. Such polypeptides include At4g08920 (SEQID NO:1497), Ceres ANNOT ID no. 1443463 (SEQ ID NO:1499), Public GI IDno. 13605525 (SEQ ID NO:1502), Public GI ID no. 94965681 (SEQ IDNO:1506), Public GI ID no. 28201254 (SEQ ID NO:1512), Ceres ANNOT ID no.1504954 (SEQ ID NO:1501), Public GI ID no. 2499553 (SEQ ID NO:1503),Public GI ID no. 738308 (SEQ ID NO:1504), Public GI ID no. 4325368 (SEQID NO:1505), Ceres CLONE ID no. 919923 (SEQ ID NO:1508), Ceres CLONE IDno. 1659764 (SEQ ID NO:1510), Public GI ID no. 125539984 (SEQ IDNO:1511). Public GI ID no. 21740729 (SEQ ID NO:1513), Public GI ID no.115458700 (SEQ ID NO:1514), Public GI ID no. 125590574 (SEQ ID NO:1515),Public GI ID no. 16444957 (SEQ ID NO:1516), Ceres CLONE ID no. 1784494(SEQ ID NO:1518), Public GI ID no. 77963980 (SEQ ID NO:1519), Public GIID no. 124361190 (SEQ ID NO:1520), Public GI ID no. 37725007 (SEQ IDNO:1521), Public GI ID no. 45935258 (SEQ ID NO:1522), Public GI ID no.15559008 (SEQ ID NO:1523), Public GI ID no. 38037416 (SEQ ID NO:1524).Public GI ID no. 77963974 (SEQ ID NO:1525). Ceres ANNOT ID no. 6112581(SEQ ID NO:1527). Public GI ID no. 56553448 (SEQ ID NO:1528), Public GIID no. 23506659 (SEQ ID NO:1529). Ceres ANNOT ID no. 6118060 (SEQ IDNO:1531). Public GI ID no. 46446306 (SEQ ID NO:1532), Public GI ID no.114321405 (SEQ ID NO:1533), Public GI ID no. 83858274 (SEQ ID NO:1534),Public GI ID no. 154250969 (SEQ ID NO:1535), Public GI ID no. 83594235(SEQ ID NO:1536), and sequences identified as functional homologs of thesequences of FIG. 18, as set forth in the sequence listing.

Polypeptides are shown in the sequence listing that have HMM bit scoresgreater than 130 when fitted to an HMM generated from the amino acidsequences set forth in FIG. 19. Such polypeptides include At4g11660 (SEQID NO:1587), Ceres CLONE ID no. 1839577 (SEQ ID NO:1589), Ceres ANNOT IDno. 1491567 (SEQ ID NO:1591), Ceres CLONE ID no. 574505 (SEQ IDNO:1596), Public GI ID no. 56117815 (SEQ ID NO:1597). Public GI ID no.92874021 (SEQ ID NO:1603), Public GI ID no. 123684 (SEQ ID NO:1605).Public GI ID no. 5821136 (SEQ ID NO:1606), Ceres CLONE ID no. 283366(SEQ ID NO:1609), Public GI ID no. 16118447 (SEQ ID NO:1612), Public GIID no. 125562434 (SEQ ID NO:1614), Ceres ANNOT ID no. 1438739 (SEQ IDNO:1593), Public GI ID no. 89274218 (SEQ ID NO:1594), Public GI ID no.115521211 (SEQ ID NO:1598), Public GI ID no. 115521213 (SEQ ID NO:1599),Public GI ID no. 115521217 (SEQ ID NO:1600), Public GI ID no. 115521209(SEQ ID NO:1601), Public GI ID no. 115521215 (SEQ ID NO:1602), Public GIID no. 11386827 (SEQ ID NO:1604), Public GI ID no. 25052685 (SEQ IDNO:1607). Ceres CLONE ID no. 1440437 (SEQ ID NO:1611). Public GI ID no.125564440 (SEQ ID NO:1613), Public GI ID no. 116309817 (SEQ ID NO:1615),Public GI ID no. 125549382 (SEQ ID NO:1616), Public GI ID no. 52077317(SEQ ID NO:1617), Public GI ID no. 115477655 (SEQ ID NO:1618), Public GIID no. 42408097 (SEQ ID NO:1619), Public GI ID no. 115459982 (SEQ IDNO:1620), Public GI ID no. 33591096 (SEQ ID NO:1621), Ceres CLONE ID no.484753 (SEQ ID NO:1623), Ceres ANNOT ID no. 6035291 (SEQ ID NO:1625),and sequences identified as functional homologs of the sequences of FIG.19, as set forth in the sequence listing.

Polypeptides are shown in the sequence listing that have HMM bit scoresgreater than 570 when fitted to an HMM generated from the amino acidsequences set forth in FIG. 20. Such polypeptides include At2g45700 (SEQID NO:1635), Ceres ANNOT ID no. 1508307 (SEQ ID NO:1637), Public GI IDno. 1495267 (SEQ ID NO:1642). Public GI ID no. 87241310 (SEQ IDNO:1644), Ceres CLONE ID no. 938390 (SEQ ID NO:1646), Ceres CLONE ID no.272338 (SEQ ID NO:1648), Ceres CLONE ID no. 1993510 (SEQ ID NO:1650),Public GI ID no. 125563862 (SEQ ID NO:1651), Public GI ID no. 125605833(SEQ ID NO:1653), Public GI ID no. 6899919 (SEQ ID NO:1632). Ceres ANNOTID no. 1455110 (SEQ ID NO:1639). Ceres ANNOT ID no. 1525218 (SEQ IDNO:1641), Public GI ID no. 15231597 (SEQ ID NO:1643), Public GI ID no.125548147 (SEQ ID NO:1652), Public GI ID no. 51091343 (SEQ ID NO:1654),Public GI ID no. 115479355 (SEQ ID NO:1655), Ceres ANNOT ID no. 6042086(SEQ ID NO:1657), Ceres ANNOT ID no. 6029903 (SEQ ID NO:1659), andsequences identified as functional homologs of the sequences of FIG. 20,as set forth in the sequence listing.

Polypeptides are shown in the sequence listing that have HMM bit scoresgreater than 150 when fitted to an HMM generated from the amino acidsequences set forth in FIG. 21. Such polypeptides include At2g35940 (SEQID NO:1540), Ceres CLONE ID no. 1943265 (SEQ ID NO:1543), Ceres ANNOT IDno. 1454522 (SEQ ID NO:1547). Public GI ID no. 31323447 (SEQ IDNO:1556), Ceres CLONE ID no. 1583941 (SEQ ID NO:1561), Ceres CLONE IDno. 1792942 (SEQ ID NO:1563), Public GI ID no. 77548772 (SEQ IDNO:1565), Public GI ID no. 84453182 (SEQ ID NO:1567), Public GI ID no.31746344 (SEQ ID NO:1541), Ceres CLONE ID no. 1926640 (SEQ ID NO:1545),Ceres ANNOT ID no. 1475125 (SEQ ID NO:1549). Ceres ANNOT ID no. 1439653(SEQ ID NO:1551), Ceres ANNOT ID no. 1461995 (SEQ ID NO:1553), Public GIID no. 13877517 (SEQ ID NO:1554), Public GI ID no. 7239157 (SEQ IDNO:1555), Public GI ID no. 22652125 (SEQ ID NO:1557), Public GI ID no.22652115 (SEQ ID NO:1558), Public GI ID no. 22652117 (SEQ ID NO:1559),Public GI ID no. 125535858 (SEQ ID NO:1564), Public GI ID no. 125578581(SEQ ID NO:1566). Public GI ID no. 13752407 (SEQ ID NO:1568), CeresANNOT ID no. 6098817 (SEQ ID NO:1570), Ceres ANNOT ID no. 6039430 (SEQID NO:1572), Ceres ANNOT ID no. 6068141 (SEQ ID NO:1574), Ceres ANNOT IDno. 6033916 (SEQ ID NO:1576), Ceres ANNOT ID no. 6034399 (SEQ IDNO:1578). Ceres ANNOT ID no. 6068617 (SEQ ID NO:1580), Ceres ANNOT IDno. 6026318 (SEQ ID NO:1582), Ceres ANNOT ID no. 6107650 (SEQ IDNO:1584), and sequences identified as functional homologs of thesequences of FIG. 21, as set forth in the sequence listing.

Polypeptides are shown in the sequence listing that have HMM bit scoresgreater than 1340 when fitted to an HMM generated from the amino acidsequences set forth in FIG. 22. Such polypeptides include At1g04400 (SEQID NO:538), Public GI ID no. 5731739 (SEQ ID NO:539), Ceres ANNOT ID no.1538045 (SEQ TD NO:541), Public GI ID no. 29467479 (SEQ ID NO:542),Public GI ID no. 133921974 (SEQ ID NO:543), Public GI ID no. 113197027(SEQ ID NO:544), Public GI ID no. 92879277 (SEQ ID NO:545), Public GI IDno. 45935260 (SEQ ID NO:546), Public GI ID no. 8101444 (SEQ ID NO:547),Public GI ID no. 78217443 (SEQ TD NO:548), Public GI ID no. 28372347(SEQ ID NO:549), Public GI ID no. 16416405 (SEQ ID NO:550), Ceres ANNOTID no. 1484634 (SEQ ID NO:552), Ceres ANNOT ID no. 1451869 (SEQ IDNO:554), Public GI ID no. 25407462 (SEQ ID NO:555), Public GI ID no.29467481 (SEQ ID NO:556), Public GI ID no. 29467477 (SEQ ID NO:557),Public GI ID no. 45935264 (SEQ ID NO:558), Public GI ID no. 5524201 (SEQID NO:559), Public GI ID no. 78217441 (SEQ ID NO:560). Public GI ID no.3551221 (SEQ ID NO:561), Public GI ID no. 3551219 (SEQ ID NO:562),Public GI ID no. 23954324 (SEQ ID NO:563), Public GI ID no. 125582937(SEQ ID NO:564), Public GI ID no. 83764373 (SEQ ID NO:565), Ceres ANNOTID no. 6045327 (SEQ ID NO:567), and sequences identified as functionalhomologs of the sequences of FIG. 22, as set forth in the sequencelisting.

Polypeptides are shown in the sequence listing that have HMM bit scoresgreater than 80 when fitted to an HMM generated from the amino acidsequences set forth in FIG. 23. Such polypeptides include At3g45610 (SEQID NO:606), Public GI ID no. 92873064 (SEQ ID NO:607), Public GI ID no.37051125 (SEQ ID NO:608), Public GI ID no. 112363376 (SEQ ID NO:609),Ceres CLONE ID no. 1938524 (SEQ ID NO:611), Ceres ANNOT ID no. 1473601(SEQ ID NO:613), Ceres ANNOT ID no. 1468397 (SEQ ID NO:615), Public GIID no. 21554185 (SEQ ID NO:616), Public GI ID no. 18424330 (SEQ IDNO:617), Public GI ID no. 8885571 (SEQ ID NO:618), Ceres CLONE ID no.20852 (SEQ ID NO:620), Public GI ID no. 21553763 (SEQ ID NO:621), PublicGI ID no. 18401763 (SEQ ID NO:622), Ceres CLONE ID no. 16423 (SEQ IDNO:624), Public GI ID no. 112363380 (SEQ ID NO:625), Public GI ID no.6092016 (SEQ ID NO:626), Ceres CLONE ID no. 770468 (SEQ ID NO:628),Public GI ID no. 113205234 (SEQ ID NO:629), Ceres ANNOT ID no. 6094775(SEQ ID NO:631), and sequences identified as functional homologs of thesequences of FIG. 23, as set forth in the sequence listing.

Polypeptides are shown in the sequence listing that have HMM bit scoresgreater than 110 when fitted to an HMM generated from the amino acidsequences set forth in FIG. 24. Such polypeptides include At4g08330 (SEQID NO:570), Ceres CLONE ID no. 1919714 (SEQ ID NO:572), Ceres ANNOT IDno. 1443290 (SEQ TD NO:574), Ceres CLONE ID no. 1042157 (SEQ ID NO:576),Ceres CLONE ID no. 1384304 (SEQ ID NO:578), Public GI ID no. 115464375(SEQ ID NO:579), Ceres CLONE ID no. 100028078 (SEQ ID NO:580), CeresANNOT ID no. 1452096 (SEQ ID NO:582), Ceres ANNOT ID no. 1503869 (SEQ IDNO:584), Ceres ANNOT ID no. 1525651 (SEQ ID NO:586), Ceres CLONE ID no.1645639 (SEQ ID NO:588), Ceres CLONE ID no. 603237 (SEQ ID NO:590),Ceres CLONE ID no. 340925 (SEQ ID NO:592), Ceres CLONE ID no. 293238(SEQ ID NO:594), Ceres CLONE ID no. 483742 (SEQ ID NO:596), Ceres CLONEID no. 1460255 (SEQ ID NO:598), Ceres CLONE ID no. 1400107 (SEQ IDNO:600), Public GI ID no. 115440865 (SEQ ID NO:601), Ceres ANNOT ID no.6016008 (SEQ ID NO:603), and sequences identified as functional homologsof the sequences of FIG. 24, asset forth in the sequence listing.

E. Percent Identity

In some embodiments, an SD+EODFR and/or low light-tolerance polypeptidehas an amino acid sequence with at least 40% sequence identity, e.g.,50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or99% sequence identity, to one of the amino acid sequences set forth inSEQ ID NO:3, SEQ ID NO:70, SEQ ID NO:129, SEQ ID NO:317, SEQ ID NO:337,SEQ ID NO:456, SEQ ID NO:538, SEQ ID NO:570, SEQ ID NO:606, SEQ IDNO:634, SEQ ID NO:644, SEQ ID NO:850, SEQ ID NO:907, SEQ ID NO:953, SEQID NO:1024, SEQ ID NO:1047, SEQ ID NO:1151, SEQ ID NO:1277, SEQ IDNO:1347, SEQ ID NO:1457, SEQ ID NO:1497, SEQ ID NO:1540, SEQ ID NO:1587,SEQ ID NO:1630, and SEQ ID NO:1635. Polypeptides having such a percentsequence identity often have a domain indicative of an SD+EODFR and/orlow light-tolerance polypeptide and/or have an HMM bit score that isgreater than 20, as discussed above. Amino acid sequences of SD+EODFRand/or low light-tolerance polypeptides having at least 40% sequenceidentity to one of the amino acid sequences set forth in SEQ ID NO:3,SEQ ID NO:70, SEQ ID NO:129. SEQ ID NO:317, SEQ ID NO:337, SEQ IDNO:456, SEQ ID NO:538, SEQ ID NO:570, SEQ ID NO:606, SEQ ID NO:634, SEQID NO:644, SEQ ID NO:850, SEQ ID NO:907, SEQ ID NO:953, SEQ ID NO:1024,SEQ ID NO:1047, SEQ ID NO:1151, SEQ ID NO:1277, SEQ ID NO:1347, SEQ IDNO:1457, SEQ ID NO:1497, SEQ ID NO:1540, SEQ ID NO:1587, and SEQ IDNO:1635 are provided in FIGS. 1-24.

“Percent sequence identity” refers to the degree of sequence identitybetween any given reference sequence. e.g., SEQ ID NO:3, and a candidateSD+EODFR and/or low light-tolerance sequence. A candidate sequencetypically has a length that is from 80 percent to 200 percent of thelength of the reference sequence, e.g., 82, 85, 87, 89, 90, 93, 95, 97,99, 100, 105, 110, 115, 120, 130, 140, 150, 160, 170, 180, 190, or 200percent of the length of the reference sequence. A percent identity forany candidate nucleic acid or polypeptide relative to a referencenucleic acid or polypeptide can be determined as follows. A referencesequence (e.g., a nucleic acid sequence or an amino acid sequence) isaligned to one or more candidate sequences using the computer programClustalW (version 1.83, default parameters), which allows alignments ofnucleic acid or polypeptide sequences to be carried out across theirentire length (global alignment). Chenna et al., Nucleic Acids Res.,31(13):3497-500 (2003).

ClustalW calculates the best match between a reference and one or morecandidate sequences, and aligns them so that identities, similaritiesand differences can be determined. Gaps of one or more residues can beinserted into a reference sequence, a candidate sequence, or both, tomaximize sequence alignments. For fast pairwise alignment of nucleicacid sequences, the following default parameters are used: word size: 2;window size: 4; scoring method: percentage; number of top diagonals: 4;and gap penalty: 5. For multiple sequence alignment of nucleic acidsequences, the following parameters are used: gap opening penalty: 10.0;gap extension penalty: 5.0; and weight transitions: yes. For fastpairwise alignment of protein sequences, the following parameters areused: word size: 1; window size: 5; scoring method: percentage; numberof top diagonals: 5; gap penalty: 3. For multiple alignment of proteinsequences, the following parameters are used: weight matrix: blosum; gapopening penalty: 10.0; gap extension penalty: 0.05; hydrophilic gaps:on; hydrophilic residues: Gly, Pro, Ser, Asn, Asp, Gin, Glu, Arg, andLys; residue-specific gap penalties: on. The ClustalW output is asequence alignment that reflects the relationship between sequences.ClustalW can be run, for example, at the Baylor College of MedicineSearch Launcher site(searchlauncher.bcm.tmc.edu/multi-align/multi-align.html) and at theEuropean Bioinformatics Institute site on the World Wide Web(ebi.ac.uk/clustalw).

To determine percent identity of a candidate nucleic acid or amino acidsequence to a reference sequence, the sequences are aligned usingClustalW, the number of identical matches in the alignment is divided bythe length of the reference sequence, and the result is multiplied by100. It is noted that the percent identity value can be rounded to thenearest tenth. For example, 78.11, 78.12, 78.13, and 78.14 are roundeddown to 78.1, while 78.15, 78.16, 78.17, 78.18, and 78.19 are rounded upto 78.2.

In some cases, an SD+EODFR and/or low light-tolerance polypeptide has anamino acid sequence with at least 40% sequence identity, e.g., 50%, 52%,56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ ID NO:3.Amino acid sequences of polypeptides having greater than 40% sequenceidentity to the polypeptide set forth in SEQ ID NO:3 are provided inFIG. 1. Such polypeptides include Ceres CLONE TD no. 1844057 (SEQ IDNO:7), Ceres ANNOT ID no. 1469148 (SEQ ID NO:22), Public GI ID no.18390998 (SEQ ID NO:25), Ceres CLONE ID no. 1065656 (SEQ ID NO:32),Ceres CLONE ID no. 1652677 (SEQ ID NO:36), Public GI ID no. 92874556(SEQ ID NO:49), Ceres CLONE ID no. 1329161 (SEQ ID NO:53), Ceres CLONEID no. 1030378 (SEQ ID NO:55), Ceres CLONE ID no. 1413787 (SEQ IDNO:57), and Public GI ID no. 125543598 (SEQ ID NO:60).

In some cases, a SD+EODFR and/or low light-tolerance polypeptide has anamino acid sequence with at least 40% sequence identity, e.g., 50%, 52%,56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ ID NO:70.Amino acid sequences of polypeptides having greater than 40% sequenceidentity to the polypeptide set forth in SEQ ID NO:70 are provided inFIG. 2. Such polypeptides include Ceres CLONE ID no. 1975934 (SEQ IDNO:72), Ceres ANNOT ID no. 1529913 (SEQ ID NO:80), Ceres CLONE ID no.977794 (SEQ ID NO:93), Public GI ID no. 42362378 (SEQ ID NO:96), PublicGI ID no. 23899378 (SEQ ID NO:99), Public GI ID no. 15963346 (SEQ IDNO:101), Public GI ID no. 15963344+B816 (SEQ ID NO:102), Public GI IDno. 92429657 (SEQ ID NO:103), Ceres CLONE ID no. 746644 (SEQ ID NO:105),Ceres CLONE ID no. 623089 (SEQ ID NO:109), Ceres CLONE ID no. 1913678(SEQ ID NO: 115), and Public GI ID no. 115450609 (SEQ ID NO: 119).

In some cases, a SD+EODFR and/or low light-tolerance polypeptide has anamino acid sequence with at least 40% sequence identity, e.g., 50%, 52%,56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:129. Amino acid sequences of polypeptides having greater than 40%sequence identity to the polypeptide set forth in SEQ ID NO:129 areprovided in FIG. 3. Such polypeptides include Public GI ID no. 34550779(SEQ ID NO:133), Ceres CLONE ID no. 1932235 (SEQ ID NO:137), Ceres CLONEID no. 981738 (SEQ ID NO:201), Ceres CLONE ID no. 565974 (SEQ IDNO:209), Public GI ID no. 1352058 (SEQ ID NO:231), Public GI ID no.11131101 (SEQ ID NO:234), Public GI ID no. 4887018 (SEQ ID NO:236),Public GI ID no. 4887018 (SEQ ID NO:236), Ceres CLONE ID no. 644455 (SEQID NO:247), Ceres CLONE ID no. 1731500 (SEQ ID NO:270), Public GI ID no.20269063 (SEQ ID NO:300), Public GI ID no. 50404477 (SEQ ID NO:302), andPublic GI ID no. 62125392 (SEQ ID NO:303).

In some cases, a SD+EODFR and/or low light-tolerance polypeptide has anamino acid sequence with at least 40% sequence identity, e.g., 50%, 52%,56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:317. Amino acid sequences of polypeptides having greater than 40%sequence identity to the polypeptide set forth in SEQ ID NO:317 areprovided in FIG. 4. Such polypeptides include Ceres CLONE ID no. 1842125(SEQ ID NO:319), Ceres ANNOT ID no. 1461360 (SEQ ID NO:321), Ceres CLONEID no. 480906 (SEQ ID NO:327), Public GI ID no. 92889352 (SEQ IDNO:330), and Public GI ID no. 56201850 (SEQ ID NO:330).

In some cases, a SD+EODFR and/or low light-tolerance polypeptide has anamino acid sequence with at least 40% sequence identity, e.g., 50%, 52%,56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:337. Amino acid sequences of polypeptides having greater than 40%sequence identity to the polypeptide set forth in SEQ ID NO:337 areprovided in FIG. 5. Such polypeptides include At2g04240 Ceres CLONE IDno. 952050 (SEQ ID NO:339), Public GI ID no. 115477050 (SEQ ID NO:349),Public GI ID no. 87162911 (SEQ ID NO:355), Ceres CLONE ID no. 1790901(SEQ ID NO:357), Ceres CLONE ID no. 1460088 (SEQ ID NO:370), Ceres CLONEID no. 1734065 (SEQ ID NO:393), Ceres CLONE ID no. 473509 (SEQ IDNO:395), Ceres CLONE ID no. 849918 (SEQ ID NO:401), Ceres CLONE ID no.633470 (SEQ ID NO:409), Ceres CLONE ID no. 1808334 (SEQ ID NO:417), andCeres ANNOT ID no. 1525600 (SEQ ID NO:437).

In some cases, a SD+EODFR and/or low light-tolerance polypeptide has anamino acid sequence with at least 40% sequence identity, e.g., 50%, 52%,56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:456. Amino acid sequences of polypeptides having greater than 40%sequence identity to the polypeptide set forth in SEQ ID NO:456 areprovided in FIG. 6. Such polypeptides include Public GI LD no. 58430585(SEQ ID NO:457), Ceres CLONE ID no. 1842825 (SEQ ID NO:466), Ceres ANNOTID no. 1449721 (SEQ ID NO:474), Public GI ID no. 41323978 (SEQ IDNO:475), Public GI ID no. 2895186 (SEQ ID NO:478), Public GI ID no.22854950 (SEQ ID NO:481), Public GI ID no. 116010474 (SEQ ID NO:485),Public GI ID no. 4091804 (SEQ ID NO:488), Public GI ID no. 60459257 (SEQID NO:494), Public GI ID no. 45544881 (SEQ ID NO:496), Public GI ID no.36789802 (SEQ ID NO:498), Public GI ID no. 92875402 (SEQ ID NO:508),Public GI ID no. 118406898 (SEQ ID NO:510), Public GI ID no. 107770485(SEQ ID NO:511), Public GI ID no. 21655154 (SEQ ID NO:532), Public GI IDno. 90657642 (SEQ ID NO:536), and Ceres CLONE ID no. 1569555 (SEQ IDNO:1842).

In some cases, a SD+EODFR and/or low light-tolerance polypeptide has anamino acid sequence with at least 40% sequence identity, e.g., 50%, 52%,56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:634. Amino acid sequences of polypeptides having greater than 40%sequence identity to the polypeptide set forth in SEQ ID NO:634 areprovided in FIG. 7. Such polypeptides include Public GI ID no. 98961985(SEQ ID NO:637).

In some cases, a SD+EODFR and/or low light-tolerance polypeptide has anamino acid sequence with at least 40% sequence identity, e.g., 50%, 52%,56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:644. Amino acid sequences of polypeptides having greater than 40%sequence identity to the polypeptide set forth in SEQ ID NO:644 areprovided in FIG. 8. Such polypeptides include SEQ TD NO:645, Ceres CLONEID no. 1849479 (SEQ ID NO:767), Public GI ID no. 89275008 (SEQ IDNO:796), Public GI ID no. 120400525 (SEQ ID NO:797), Public GI ID no.98980426 (SEQ ID NO:804), Public GI ID no. 71983373 (SEQ ID NO:808),Public GI ID no. 41351817 (SEQ ID NO:809), Public GI ID no. 76446191(SEQ ID NO:811), Public GI ID no. 5616086 (SEQ ID NO:813), Ceres CLONEID no. 1052602 (SEQ ID NO:826), Public GI ID no. 72068957 (SEQ IDNO:830), Public GI ID no. 71534113 (SEQ ID NO:831), Public GI ID no.37147896 (SEQ TD NO:832), Public GI ID no. 92918850 (SEQ ID NO:834),Public GI ID no. 40647095 (SEQ ID NO:835), Ceres ANNOT ID no. 1527711(SEQ ID NO:837), Public GI ID no. 71041116 (SEQ ID NO:838), Public GI IDno. 12003384 (SEQ ID NO:839), Public GI ID no. 18535580 (SEQ ID NO:840),and Public GI ID no. 115353971 (SEQ ID NO:1843).

In some cases, a SD+EODFR and/or low light-tolerance polypeptide has anamino acid sequence with at least 40% sequence identity, e.g., 50%, 52%,56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:850. Amino acid sequences of polypeptides having greater than 40%sequence identity to the polypeptide set forth in SEQ ID NO:850 areprovided in FIG. 9. Such polypeptides include Ceres CLONE ID no. 1833093(SEQ ID NO:853), Ceres ANNOT ID no. 1502190 (SEQ ID NO:857), Ceres CLONEID no. 565641 (SEQ ID NO:876), Public GI ID no. 87240507 (SEQ IDNO:877), Ceres CLONE ID no. 1325382 (SEQ ID NO:881), Ceres CLONE ID no.1558265 (SEQ ID NO:885), Ceres CLONE ID no. 1823669 (SEQ ID NO:895), andPublic GI ID no. 115464921 (SEQ ID NO:898).

In some cases, a SD+EODFR and/or low light-tolerance polypeptide has anamino acid sequence with at least 40% sequence identity, e.g., 50%, 52%,56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:907. Amino acid sequences of polypeptides having greater than 40%sequence identity to the polypeptide set forth in SEQ ID NO:907 arcprovided in FIG. 10. Such polypeptides include Ceres CLONE ID no.1940797 (SEQ ID NO:909), Ceres ANNOT ID no. 1538900 (SEQ ID NO:911),Ceres CLONE ID no. 1126868 (SEQ ID NO:922), Public GI ID no. 89257684(SEQ ID NO:923), Public GI ID no. 124360460 (SEQ ID NO:929), Public GIID no. 62865694 (SEQ ID NO:931), Public GI ID no. 62865692 (SEQ IDNO:932), Ceres CLONE ID no. 260368 (SEQ ID NO:936), Ceres CLONE ID no.1873510 (SEQ ID NO:947), Public GI ID no. 125541662 (SEQ ID NO:948),Public GI ID no. 48716268 (SEQ ID NO:950), and Public GI ID no. 62865696(SEQ ID NO:1844).

In some cases, a SD+EODFR and/or low light-tolerance polypeptide has anamino acid sequence with at least 40% sequence identity, e.g., 50%, 52%,56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:953. Amino acid sequences of polypeptides having greater than 40%sequence identity to the polypeptide set forth in SEQ ID NO:953 areprovided in FIG. 11. Such polypeptides include Ceres CLONE ID no.1798705 (SEQ ID NO:955), Ceres ANNOT ID no. 1458907 (SEQ ID NO:963),Ceres CLONE ID no. 1090409 (SEQ ID NO:971), Ceres CLONE ID no. 479817(SEQ ID NO:977), Ceres CLONE ID no. 1041793 (SEQ ID NO:979), Ceres CLONEID no. 684633 (SEQ ID NO:985), Ceres CLONE ID no. 371815 (SEQ IDNO:991), Ceres CLONE ID no. 1686460 (SEQ ID NO:993), Ceres CLONE ID no.1448595 (SEQ ID NO:995), Ceres CLONE ID no. 1734477 (SEQ ID NO:999),Ceres CLONE ID no. 1605693 (SEQ ID NO:1005), Ceres CLONE ID no. 1757400(SEQ ID NO:1009), and Public GI ID no. 115434334 (SEQ ID NO:1015).

In some cases, a SD+EODFR and/or low light-tolerance polypeptide has anamino acid sequence with at least 40% sequence identity, e.g., 50%, 52%,56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1024. Amino acid sequences of polypeptides having greater than 40%sequence identity to the polypeptide set forth in SEQ ID NO:1024 areprovided in FIG. 12. Such polypeptides include Ceres ANNOT ID no.1452905 (SEQ ID NO:1029), Ceres CLONE ID no. 956176 (SEQ ID NO:1039),Public GI ID no. 92870366 (SEQ ID NO:1040), Ceres CLONE ID no. 294166(SEQ ID NO:1042), and Public GI ID no. 125543067 (SEQ ID NO:1043).

In some cases, an SD+EODFR and/or low light-tolerance polypeptide has anamino acid sequence with at least 40% sequence identity, e.g., 50%, 52%,56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1047. Amino acid sequences of polypeptides having greater than 40%sequence identity to the polypeptide set forth in SEQ ID NO:1047 areprovided in FIG. 13. Such polypeptides include Ceres CLONE ID no.1837694 (SEQ ID NO:1053), Ceres ANNOT ID no. 1483367 (SEQ ID NO:1057).Ceres CLONE ID no. 1077781 (SEQ ID NO:1083). Ceres CLONE ID no. 471026(SEQ ID NO:1085), Public GI ID no. 92888885 (SEQ ID NO:1099), Public GIID no. 45544873 (SEQ ID NO:1100), Public GI ID no. 45758663 (SEQ IDNO:1101), Ceres CLONE ID no. 772927 (SEQ ID NO:1105), Ceres CLONE ID no.895080 (SEQ ID NO: 1111), Ceres CLONE ID no. 1806128 (SEQ ID NO:1131),Public GI ID no. 115458192 (SEQ ID NO: 1134), and Public GI ID no.82470795 (SEQ ID NO:1139).

In some cases, a SD+EODFR and/or low light-tolerance polypeptide has anamino acid sequence with at least 40% sequence identity, e.g., 50%, 52%,56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1151. Amino acid sequences of polypeptides having greater than 40%sequence identity to the polypeptide set forth in SEQ ID NO:1151 areprovided in FIG. 14. Such polypeptides include Ceres CLONE ID no.1851526 (SEQ ID NO: 1155), Ceres ANNOT ID no. 1486769 (SEQ ID NO: 1172).Public GI ID no. 83032232 (SEQ ID NO:1209), Ceres CLONE ID no. 1620420(SEQ ID NO:1211), Public GI ID no. 92892428 (SEQ ID NO:1215), CeresCLONE ID no. 884742 (SEQ ID NO:1223), Ceres CLONE ID no. 1821559 (SEQ IDNO:1246), Public GI ID no. 51535021 (SEQ ID NO:1258). Public GI ID no.113205304 (SEQ ID NO:1263), and Public GI ID no. 37719051 (SEQ IDNO:1264).

In some cases, a SD+EODFR and/or low light-tolerance polypeptide has anamino acid sequence with at least 40% sequence identity, e.g., 50%, 52%,56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1277. Amino acid sequences of polypeptides having greater than 40%sequence identity to the polypeptide set forth in SEQ ID NO:1277 areprovided in FIG. 15. Such polypeptides include Ceres CLONE ID no.1926352 (SEQ ID NO:1279), Ceres ANNOT ID no. 1448905 (SEQ ID NO:1285),Public GI ID no. 15236865 (SEQ ID NO:1294), Ceres CLONE ID no. 934771(SEQ ID NO:1301), Ceres CLONE ID no. 338386 (SEQ ID NO:1303), CeresCLONE ID no. 1780691 (SEQ ID NO:1317), and Public GI ID no. 115464819(SEQ ID NO:1326).

In some cases, a SD+EODFR and/or low light-tolerance polypeptide has anamino acid sequence with at least 40% sequence identity, e.g., 50%, 52%,56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1347. Amino acid sequences of polypeptides having greater than 40%sequence identity to the polypeptide set forth in SEQ ID NO:1347 areprovided in FIG. 16. Such polypeptides include Ceres CLONE ID no. 285028(SEQ ID NO:1419), Ceres CLONE ID no. 100969565 (SEQ ID NO:1422), PublicGI ID no. 1352057 (SEQ ID NO:1427), Ceres ANNOT ID no. 1453784 (SEQ IDNO:1429), Public GI ID no. 452777 (SEQ ID NO:1430), and Public GI ID no.92873297 (SEQ ID NO:1431).

In some cases, a SD+EODFR and/or low light-tolerance polypeptide has anamino acid sequence with at least 40% sequence identity, e.g., 50%, 52%,56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 900%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1457. Amino acid sequences of polypeptides having greater than 40%sequence identity to the polypeptide set forth in SEQ ID NO:1457 areprovided in FIG. 17. Such polypeptides include Ceres CLONE ID no.1924904 (SEQ ID NO:1460), Ceres ANNOT ID no. 1543346 (SEQ ID NO:1462).Public GI ID no. 18396338 (SEQ ID NO:1467), Ceres CLONE ID no. 833872(SEQ ID NO:1471), Ceres CLONE ID no. 1579587 (SEQ ID NO:1475), CeresCLONE ID no. 1786411 (SEQ ID NO:1477), and Public GI ID no. 108864370(SEQ ID NO:1480).

In some cases, a SD+EODFR and/or low light-tolerance polypeptide has anamino acid sequence with at least 40% sequence identity, e.g., 50%, 52%,56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1497. Amino acid sequences of polypeptides having greater than 40%sequence identity to the polypeptide set forth in SEQ ID NO:1497 areprovided in FIG. 18. Such polypeptides include Ceres ANNOT ID no.1443463 (SEQ ID NO:1499), Public GI ID no. 13605525 (SEQ ID NO:1502),Public GI ID no. 94965681 (SEQ ID NO:1506), and Public GI ID no.28201254 (SEQ ID NO:1512).

In some cases, a SD+EODFR and/or low light-tolerance polypeptide has anamino acid sequence with at least 40% sequence identity, e.g., 50%, 52%,56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1587. Amino acid sequences of polypeptides having greater than 40%sequence identity to the polypeptide set forth in SEQ ID NO:1587 areprovided in FIG. 19. Such polypeptides include Ceres CLONE ID no.1839577 (SEQ ID NO:1589), Ceres ANNOT ID no. 1491567 (SEQ ID NO:1591).Ceres CLONE ID no. 574505 (SEQ ID NO:1596). Public GI ID no. 56117815(SEQ ID NO:1597), Public GI ID no. 92874021 (SEQ ID NO:1603), Public GIID no. 123684 (SEQ ID NO:1605), Public GI ID no. 5821136 (SEQ IDNO:1606), Ceres CLONE ID no. 283366 (SEQ ID NO:1609), Public GI ID no.16118447 (SEQ ID NO:1612), and Public GI ID no. 125562434 (SEQ IDNO:1614).

In some cases, a SD+EODFR and/or low light-tolerance polypeptide has anamino acid sequence with at least 40% sequence identity, e.g., 50%, 52%,56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 900%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1635. Amino acid sequences of polypeptides having greater than 40%sequence identity to the polypeptide set forth in SEQ ID NO:1635 areprovided in FIG. 20. Such polypeptides include Ceres ANNOT ID no.1508307 (SEQ ID NO:1637), Public GI ID no. 1495267 (SEQ ID NO:1642).Public GI ID no. 87241310 (SEQ ID NO:1644), Ceres CLONE ID no. 938390(SEQ ID NO:1646), Ceres CLONE ID no. 272338 (SEQ ID NO:1648), CeresCLONE ID no. 1993510 (SEQ ID NO:1650), Public GI ID no. 125563862 (SEQID NO:1651), and Public GI ID no. 125605833 (SEQ ID NO:1653).

In some cases, a SD+EODFR and/or low light-tolerance polypeptide has anamino acid sequence with at least 40% sequence identity, e.g., 50%, 52%,56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1540. Amino acid sequences of polypeptides having greater than 40%sequence identity to the polypeptide set forth in SEQ ID NO:1540 areprovided in FIG. 21. Such polypeptides include Ceres CLONE ID no.1943265 (SEQ ID NO:1543), Ceres ANNOT ID no. 1454522 (SEQ ID NO:1547),Public GI ID no. 31323447 (SEQ ID NO:1556), Ceres CLONE ID no. 1583941(SEQ ID NO:1561), Ceres CLONE ID no. 1792942 (SEQ ID NO:1563), Public GIID no. 77548772 (SEQ ID NO:1565), and Public GI ID no. 84453182 (SEQ IDNO:1567).

In some cases, a SD+EODFR and/or low light-tolerance polypeptide has anamino acid sequence with at least 40% sequence identity, e.g., 50%, 52%,56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:538. Amino acid sequences of polypeptides having greater than 40%sequence identity to the polypeptide set forth in SEQ ID NO:538 areprovided in FIG. 22. Such polypeptides include Public GI ID no. 5731739(SEQ ID NO:539), Ceres ANNOT ID no. 1538045 (SEQ ID NO:541), Public GIID no. 29467479 (SEQ ID NO:542), Public GI ID no. 133921974 (SEQ TDNO:543), Public GI ID no. 113197027 (SEQ ID NO:544), Public GI ID no.92879277 (SEQ ID NO:545), Public GI ID no. 45935260 (SEQ ID NO:546),Public GI ID no. 8101444 (SEQ ID NO:547), Public GI ID no. 78217443 (SEQID NO:548), and Public GI ID no. 28372347 (SEQ ID NO:549).

In some cases, a SD+EODFR and/or low light-tolerance polypeptide has anamino acid sequence with at least 40% sequence identity, e.g., 50%, 52%,56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 900%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:606. Amino acid sequences of polypeptides having greater than 40%sequence identity to the polypeptide set forth in SEQ ID NO:606 areprovided in FIG. 23. Such polypeptides include Public GI ID no. 92873064(SEQ ID NO:607), Public GI ID no. 37051125 (SEQ ID NO:608), and PublicGI ID no. 112363376 (SEQ ID NO:609).

In some cases, a SD+EODFR and/or low light-tolerance polypeptide has anamino acid sequence with at least 40% sequence identity, e.g., 50%, 52%,56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:570. Amino acid sequences of polypeptides having greater than 40%sequence identity to the polypeptide set forth in SEQ ID NO:570 areprovided in FIG. 24. Such polypeptides include Ceres CLONE ID no.1919714 (SEQ ID NO:572), Ceres ANNOT ID no. 1443290 (SEQ ID NO:574),Ceres CLONE ID no. 1042157 (SEQ ID NO:576), Ceres CLONE ID no. 1384304(SEQ ID NO:578), and Public GI ID no. 115464375 (SEQ ID NO:579).

In some cases, a red light specific response pathway polypeptide has anamino acid sequence with at least 40% sequence identity, e.g., 50%, 52%,56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:456. Amino acid sequences of polypeptides having greater than 40%sequence identity to the polypeptide set forth in SEQ ID NO:456 areprovided in FIG. 6. Such polypeptides include Public GI ID no. 58430585(SEQ ID NO:457), Ceres CLONE ID no. 1842825 (SEQ ID NO:466), Ceres ANNOTID no. 1449721 (SEQ ID NO:474), Public GI ID no. 41323978 (SEQ IDNO:475), Public GI ID no. 2895186 (SEQ ID NO:478), Public GI ID no.22854950 (SEQ ID NO:481), Public GI ID no. 116010474 (SEQ ID NO:485),Public GI ID no. 4091804 (SEQ ID NO:488), Public GI ID no. 60459257 (SEQID NO:494), Public GI ID no. 45544881 (SEQ ID NO:496), Public GI ID no.36789802 (SEQ ID NO:498), Public GI ID no. 92875402 (SEQ ID NO:508),Public GI ID no. 118406898 (SEQ ID NO:510), Public GI ID no. 107770485(SEQ ID NO:511), Public GI ID no. 21655154 (SEQ ID NO:532), Public GI IDno. 90657642 (SEQ ID NO:536), and Ceres CLONE ID no. 1569555 (SEQ IDNO:1842).

In some cases, red light specific response pathway polypeptide has anamino acid sequence with at least 40% sequence identity, e.g., 50%, 52%,56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:953. Amino acid sequences of polypeptides having greater than 40%sequence identity to the polypeptide set forth in SEQ ID NO:953 areprovided in FIG. 11. Such polypeptides include Ceres CLONE ID no.1798705 (SEQ ID NO:955), Ceres ANNOT ID no. 1458907 (SEQ ID NO:963),Ceres CLONE ID no. 1090409 (SEQ ID NO:971), Ceres CLONE ID no. 479817(SEQ ID NO:977), Ceres CLONE ID no. 1041793 (SEQ ID NO:979), Ceres CLONEID no. 684633 (SEQ ID NO:985), Ceres CLONE ID no. 371815 (SEQ IDNO:991), Ceres CLONE ID no. 1686460 (SEQ ID NO:993), Ceres CLONE ID no.1448595 (SEQ ID NO:995), Ceres CLONE LD no. 1734477 (SEQ ID NO:999),Ceres CLONE ID no. 1605693 (SEQ ID NO:1005), Ceres CLONE ID no. 1757400(SEQ ID NO:1009), and Public GI ID no. 115434334 (SEQ ID NO:1015).

In some cases, a red light specific response pathway polypeptide has anamino acid sequence with at least 40% sequence identity, e.g., 50%, 52%,56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1540. Amino acid sequences of polypeptides having greater than 40%sequence identity to the polypeptide set forth in SEQ ID NO:1540 areprovided in FIG. 21. Such polypeptides include Ceres CLONE ID no.1943265 (SEQ ID NO:1543), Ceres ANNOT ID no. 1454522 (SEQ ID NO:1547),Public GI LD no. 31323447 (SEQ ID NO:1556), Ceres CLONE ID no. 1583941(SEQ ID NO:1561), Ceres CLONE ID no. 1792942 (SEQ ID NO:1563), Public GIID no. 77548772 (SEQ ID NO:1565), and Public GI ID no. 84453182 (SEQ IDNO:1567).

F. Other Sequences

It should be appreciated that an SD+EODFR and/or low light-tolerancepolypeptide and red light specific response pathway polypeptide caninclude additional amino acids that are not involved in an SD+EODFRand/or low light tolerance, or a red light specific response pathway,and thus such a polypeptide can be longer than would otherwise be thecase. For example, an SD+EODFR and/or low light-tolerance polypeptidecan include a purification tag, a chloroplast transit peptide, amitochondrial transit peptide, an amyloplast peptide, or a leadersequence added to the amino or carboxy terminus. In some embodiments, anSD+EODFR and/or low light-tolerance polypeptide includes an amino acidsequence that functions as a reporter, e.g., a green fluorescent proteinor yellow fluorescent protein.

III. NUCLEIC ACIDS

Nucleic acids described herein include nucleic acids that are effectiveto modulate SD+EODFR and/or low light tolerance when transcribed in aplant or plant cell. Such nucleic acids include, without limitation,those that encode an SD+EODFR and/or low light-tolerance polypeptide andthose that can be used to inhibit expression of an SD+EODFR and/or lowlight-tolerance polypeptide or a red light specific response pathwaypolypeptide via a nucleic acid based method.

A. Nucleic Acids Encoding SD+EODFR and/or Low Light-TolerancePolypeptides

Nucleic acids encoding SD+EODFR and/or low light-tolerance polypeptidesare described herein. Such nucleic acids include SEQ ID NOs:1, 2, 4, 6,8, 11, 13, 15, 17, 19, 21, 23, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45,47, 50, 52, 54, 56, 58, 64, 66, 68, 69, 71, 73, 75, 77, 79, 81, 83, 85,87, 92, 94, 104, 106, 108, 110, 112, 114, 123, 125, 127, 128, 134, 136,138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164,166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 190, 192, 194,196, 198, 200, 202, 204, 206, 208, 210, 212, 214, 216, 218, 220, 222,224, 226, 228, 240, 242, 244, 246, 248, 250, 252, 254, 256, 258, 260,263, 265, 267, 269, 272, 274, 276, 278, 280, 282, 284, 286, 288, 290,305, 307, 309, 311, 313, 315, 316, 318, 320, 322, 324, 326, 328, 333,335, 336, 338, 340, 342, 345, 356, 358, 360, 363, 369, 371, 373, 375,377, 380, 382, 384, 386, 388, 390, 392, 394, 396, 398, 400, 402, 404,406, 408, 410, 412, 414, 416, 418, 420, 422, 424, 426, 428, 430, 432,434, 436, 438, 440, 442, 444, 446, 448, 450, 452, 454, 455, 461, 463,465, 467, 469, 471, 473, 476, 490, 492, 500, 502, 504, 506, 513, 517,519, 537, 540, 551, 553, 566, 568, 569, 571, 573, 575, 577, 581, 583,585, 587, 589, 591, 593, 595, 597, 599, 602, 604, 605, 610, 612, 614,619, 623, 627, 630, 632, 633, 635, 640, 642, 643, 646, 648, 650, 652,654, 656, 658, 660, 662, 664, 666, 668, 670, 672, 674, 677, 679, 681,683, 685, 687, 689, 691, 693, 696, 698, 700, 703, 705, 707, 710, 715,717, 719, 722, 724, 727, 729, 731, 733, 735, 737, 739, 746, 748, 752,754, 756, 758, 760, 766, 768, 770, 772, 775, 777, 781, 785, 787, 789,791, 793, 825, 828, 836, 842, 844, 846, 848, 849, 852, 854, 856, 858,860, 867, 869, 871, 873, 875, 878, 880, 882, 884, 886, 888, 890, 892,894, 896, 899, 901, 903, 905, 906, 908, 910, 912, 914, 916, 918, 921,925, 927, 933, 935, 942, 944, 946, 951, 952, 954, 956, 958, 960, 962,964, 968, 970, 972, 974, 976, 978, 980, 982, 984, 986, 988, 990, 992,994, 996, 998, 1000, 1002, 1004, 1006, 1008, 1010, 1012, 1017, 1019,1020, 1021, 1022, 1023, 1026, 1028, 1031, 1034, 1036, 1038, 1041, 1045,1046, 1048, 1050, 1052, 1054, 1056, 1058, 1060, 1062, 1064, 1066, 1070,1076, 1079, 1082, 1084, 1086, 1088, 1090, 1092, 1094, 1096, 1102, 1104,1106, 1108, 1110, 1112, 1114, 1116, 1118, 1120, 1122, 1124, 1126, 1128,1130, 1132, 1140, 1142, 1144, 1146, 1148, 1150, 1152, 1154, 1156, 1158,1163, 1165, 1167, 1169, 1171, 1173, 1175, 1177, 1179, 1181, 1183, 1185,1187, 1189, 1191, 1193, 1195, 1197, 1205, 1207, 1210, 1212, 1218, 1220,1222, 1224, 1226, 1228, 1231, 1233, 1235, 1237, 1239, 1241, 1243, 1245,1247, 1249, 1251, 1253, 1265, 1267, 1269, 1271, 1273, 1275, 1276, 1278,1280, 1282, 1284, 1286, 1288, 1290, 1292, 1296, 1300, 1302, 1304, 1306,1308, 1310, 1312, 1314, 1316, 1318, 1320, 1333, 1335, 1337, 1339, 1341,1343, 1345, 1346, 1348, 1350, 1354, 1356, 1359, 1361, 1363, 1365, 1369,1371, 1373, 1376, 1378, 1380, 1382, 1384, 1386, 1388, 1390, 1392, 1394,1396, 1398, 1400, 1403, 1405, 1407, 1409, 1416, 1418, 1420, 1428, 1432,1437, 1441, 1443, 1445, 1447, 1449, 1451, 1453, 1454, 1455, 1456, 1459,1461, 1463, 1465, 1470, 1472, 1474, 1476, 1487, 1489, 1491, 1493, 1495,1496, 1498, 1500, 1507, 1509, 1517, 1526, 1530, 1537, 1538, 1539, 1542,1544, 1546, 1548, 1550, 1552, 1560, 1562, 1569, 1571, 1573, 1575, 1577,1579, 1581, 1583, 1585, 1586, 1588, 1590, 1592, 1595, 1608, 1610, 1622,1624, 1626, 1627, 1628, 1629, 1633, 1634, 1636, 1638, 1640, 1645, 1647,1649, 1656, 1658, 1660, 1662, 1664, 1666, 1668, 1670, 1672, 1674, 1676,1678, 1680, 1683, 1685, 1687, 1689, 1691, 1693, 1695, 1697, 1706, 1708,1710, 1712, 1714, 1716, 1718, 1724, 1726, 1728, 1731, 1733, 1735, 1737,1747, 1749, 1753, 1755, 1757, 1759, 1761, 1763, 1765, 1779, 1781, 1783,1785, 1787, 1789, 1791, 1793, 1795, 1797, 1799, 1801, 1803, 1841, 1849,1851, 1853, 1855, 1857, 1868, 1872, 1874, 1876, 1878, 1880, 1882, 1884,1886, 1888, 1890, 1892, 1894, 1896, 1898, 1900, 1902, 1904, 1906, 1908,1910, 1912, 1914, 1916, 1918, 1920, 1922, 1924, 1926, 1928, 1930, 1932,1934, 1936, 1938, 1940, 1942, 1944, 1946, 1948, 1950, 1952, 1954, 1956,1958, 1960, 1962, 1964, 1966, 1968, 1970, 1972, 1974, 1976, 1978, 1980,1982, 1984, 1986, 1988, 1990, 1992, 1994, 1996, 1998, 2000, 2002, 2004,2006, 2008, 2010, 2012, 2014, 2016, 2018, 2020, 2022, 2024, 2026, 2028,2068, 2071, 2073, 2075, 2077, 2079, 2082, 2086, 2088, 2090, 2092, 2094,2096, 2098, 2100, 2102, 2104, 2106, 2108, 2110, 2112, 2122, 2124, 2126,2128, 2130, 2132, 2134, 2145, 2147, 2149, 2151, 2153, 2155, 2157, 2159,2161, 2163, 2165, 2167, 2169, 2171, 2173, 2175, 2177, 2179, 2181, 2265,2267, 2279, 2281, 2283, 2285, 2287, 2289, 2291, 2293, 2295, 2297, 2299,2301, 2303, 2305, 2307, 2309, 2311, 2313, 2315, 2317, 2319, 2321, 2349,2351, 2353, 2355, 2357, 2359, 2361, 2363, 2365, 2367, 2369, 2371, and2373 as described in more detail below. A nucleic acid also can be afragment that is at least 40% (e.g., at least 45, 50, 55, 60, 65, 70,75, 80, 85, 90, 95, or 99%) of the length of the full-length nucleicacid set forth in SEQ ID NOs:1, 2, 4, 6, 8, 11, 13, 15, 17, 19, 21, 23,27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 50, 52, 54, 56, 58, 64, 66,68, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 92, 94, 104, 106, 108, 110,112, 114, 123, 125, 127, 128, 134, 136, 138, 140, 142, 144, 146, 148,150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176,178, 180, 182, 184, 186, 190, 192, 194, 196, 198, 200, 202, 204, 206,208, 210, 212, 214, 216, 218, 220, 222, 224, 226, 228, 240, 242, 244,246, 248, 250, 252, 254, 256, 258, 260, 263, 265, 267, 269, 272, 274,276, 278, 280, 282, 284, 286, 288, 290, 305, 307, 309, 311, 313, 315,316, 318, 320, 322, 324, 326, 328, 333, 335, 336, 338, 340, 342, 345,356, 358, 360, 363, 369, 371, 373, 375, 377, 380, 382, 384, 386, 388,390, 392, 394, 396, 398, 400, 402, 404, 406, 408, 410, 412, 414, 416,418, 420, 422, 424, 426, 428, 430, 432, 434, 436, 438, 440, 442, 444,446, 448, 450, 452, 454, 455, 461, 463, 465, 467, 469, 471, 473, 476,490, 492, 500, 502, 504, 506, 513, 517, 519, 537, 540, 551, 553, 566,568, 569, 571, 573, 575, 577, 581, 583, 585, 587, 589, 591, 593, 595,597, 599, 602, 604, 605, 610, 612, 614, 619, 623, 627, 630, 632, 633,635, 640, 642, 643, 646, 648, 650, 652, 654, 656, 658, 660, 662, 664,666, 668, 670, 672, 674, 677, 679, 681, 683, 685, 687, 689, 691, 693,696, 698, 700, 703, 705, 707, 710, 715, 717, 719, 722, 724, 727, 729,731, 733, 735, 737, 739, 746, 748, 752, 754, 756, 758, 760, 766, 768,770, 772, 775, 777, 781, 785, 787, 789, 791, 793, 825, 828, 836, 842,844, 846, 848, 849, 852, 854, 856, 858, 860, 867, 869, 871, 873, 875,878, 880, 882, 884, 886, 888, 890, 892, 894, 896, 899, 901, 903, 905,906, 908, 910, 912, 914, 916, 918, 921, 925, 927, 933, 935, 942, 944,946, 951, 952, 954, 956, 958, 960, 962, 964, 968, 970, 972, 974, 976,978, 980, 982, 984, 986, 988, 990, 992, 994, 996, 998, 1000, 1002, 1004,1006, 1008, 1010, 1012, 1017, 1019, 1020, 1021, 1022, 1023, 1026, 1028,1031, 1034, 1036, 1038, 1041, 1045, 1046, 1048, 1050, 1052, 1054, 1056,1058, 1060, 1062, 1064, 1066, 1070, 1076, 1079, 1082, 1084, 1086, 1088,1090, 1092, 1094, 1096, 1102, 1104, 1106, 1108, 1110, 1112, 1114, 1116,1118, 1120, 1122, 1124, 1126, 1128, 1130, 1132, 1140, 1142, 1144, 1146,1148, 1150, 1152, 1154, 1156, 1158, 1163, 1165, 1167, 1169, 1171, 1173,1175, 1177, 1179, 1181, 1183, 1185, 1187, 1189, 1191, 1193, 1195, 1197,1205, 1207, 1210, 1212, 1218, 1220, 1222, 1224, 1226, 1228, 1231, 1233,1235, 1237, 1239, 1241, 1243, 1245, 1247, 1249, 1251, 1253, 1265, 1267,1269, 1271, 1273, 1275, 1276, 1278, 1280, 1282, 1284, 1286, 1288, 1290,1292, 1296, 1300, 1302, 1304, 1306, 1308, 1310, 1312, 1314, 1316, 1318,1320, 1333, 1335, 1337, 1339, 1341, 1343, 1345, 1346, 1348, 1350, 1354,1356, 1359, 1361, 1363, 1365, 1369, 1371, 1373, 1376, 1378, 1380, 1382,1384, 1386, 1388, 1390, 1392, 1394, 1396, 1398, 1400, 1403, 1405, 1407,1409, 1416, 1418, 1420, 1428, 1432, 1437, 1441, 1443, 1445, 1447, 1449,1451, 1453, 1454, 1455, 1456, 1459, 1461, 1463, 1465, 1470, 1472, 1474,1476, 1487, 1489, 1491, 1493, 1495, 1496, 1498, 1500, 1507, 1509, 1517,1526, 1530, 1537, 1538, 1539, 1542, 1544, 1546, 1548, 1550, 1552, 1560,1562, 1569, 1571, 1573, 1575, 1577, 1579, 1581, 1583, 1585, 1586, 1588,1590, 1592, 1595, 1608, 1610, 1622, 1624, 1626, 1627, 1628, 1629, 1633,1634, 1636, 1638, 1640, 1645, 1647, 1649, 1656, 1658, 1660, 1662, 1664,1666, 1668, 1670, 1672, 1674, 1676, 1678, 1680, 1683, 1685, 1687, 1689,1691, 1693, 1695, 1697, 1706, 1708, 1710, 1712, 1714, 1716, 1718, 1724,1726, 1728, 1731, 1733, 1735, 1737, 1747, 1749, 1753, 1755, 1757, 1759,1761, 1763, 1765, 1779, 1781, 1783, 1785, 1787, 1789, 1791, 1793, 1795,1797, 1799, 1801, 1803, 1841, 1849, 1851, 1853, 1855, 1857, 1868, 1872,1874, 1876, 1878, 1880, 1882, 1884, 1886, 1888, 1890, 1892, 1894, 1896,1898, 1900, 1902, 1904, 1906, 1908, 1910, 1912, 1914, 1916, 1918, 1920,1922, 1924, 1926, 1928, 1930, 1932, 1934, 1936, 1938, 1940, 1942, 1944,1946, 1948, 1950, 1952, 1954, 1956, 1958, 1960, 1962, 1964, 1966, 1968,1970, 1972, 1974, 1976, 1978, 1980, 1982, 1984, 1986, 1988, 1990, 1992,1994, 1996, 1998, 2000, 2002, 2004, 2006, 2008, 2010, 2012, 2014, 2016,2018, 2020, 2022, 2024, 2026, 2028, 2068, 2071, 2073, 2075, 2077, 2079,2082, 2086, 2088, 2090, 2092, 2094, 2096, 2098, 2100, 2102, 2104, 2106,2108, 2110, 2112, 2122, 2124, 2126, 2128, 2130, 2132, 2134, 2145, 2147,2149, 2151, 2153, 2155, 2157, 2159, 2161, 2163, 2165, 2167, 2169, 2171,2173, 2175, 2177, 2179, 2181, 2265, 2267, 2279, 2281, 2283, 2285, 2287,2289, 2291, 2293, 2295, 2297, 2299, 2301, 2303, 2305, 2307, 2309, 2311,2313, 2315, 2317, 2319, 2321, 2349, 2351, 2353, 2355, 2357, 2359, 2361,2363, 2365, 2367, 2369, 2371, and 2373.

An SD+EODFR and/or low light-tolerance nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:1 or SEQ ID NO:2.Alternatively, an SD+EODFR and/or low light-tolerance nucleic acid canbe a variant of the nucleic acid having the nucleotide sequence setforth in SEQ ID NO:1 or SEQ ID NO:2. For example, an SD+EODFR and/or lowlight-tolerance nucleic acid can have a nucleotide sequence with atleast 80% sequence identity, e.g., 81%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the nucleotide sequence set forth in SEQ ID NO:1or SEQ ID NO:2.

An SD+EODFR and/or low light-tolerance nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:68 or SEQ ID NO:69.Alternatively, an SD+EODFR and/or low light-tolerance nucleic acid canbe a variant of the nucleic acid having the nucleotide sequence setforth in SEQ ID NO:68 or SEQ ID NO:69. For example, an SD+EODFR and/orlow light-tolerance nucleic acid can have a nucleotide sequence with atleast 80% sequence identity, e.g., 81%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the nucleotide sequence set forth in SEQ ID NO:68or SEQ ID NO:69.

An SD+EODFR and/or low light-tolerance nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:127 or SEQ ID NO:128.Alternatively, an SD+EODFR and/or low light-tolerance nucleic acid canbe a variant of the nucleic acid having the nucleotide sequence setforth in SEQ ID NO:127 or SEQ ID NO:128. For example, an SD+EODFR and/orlow light-tolerance nucleic acid can have a nucleotide sequence with atleast 80% sequence identity, e.g., 81%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the nucleotide sequence set forth in SEQ ID NO:127or SEQ ID NO:128.

An SD+EODFR and/or low light-tolerance nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:315 or SEQ ID NO:316.Alternatively, an SD+EODFR and/or low light-tolerance nucleic acid canbe a variant of the nucleic acid having the nucleotide sequence setforth in SEQ ID NO:315 or SEQ ID NO:316. For example, an SD+EODFR and/orlow light-tolerance nucleic acid can have a nucleotide sequence with atleast 80% sequence identity, e.g., 81%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the nucleotide sequence set forth in SEQ ID NO:315or SEQ ID NO:316.

An SD+EODFR and/or low light-tolerance nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:335 or SEQ ID NO:336.Alternatively, an SD+EODFR and/or low light-tolerance nucleic acid canbe a variant of the nucleic acid having the nucleotide sequence setforth in SEQ ID NO:335 or SEQ ID NO:336. For example, an SD+EODFR and/orlow light-tolerance nucleic acid can have a nucleotide sequence with atleast 80% sequence identity, e.g., 81%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the nucleotide sequence set forth in SEQ ID NO:335or SEQ ID NO:336.

An SD+EODFR and/or low light-tolerance nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:454 or SEQ ID NO:455.Alternatively, an SD+EODFR and/or low light-tolerance nucleic acid canbe a variant of the nucleic acid having the nucleotide sequence setforth in SEQ ID NO:454 or SEQ ID NO:455. For example, an SD+EODFR and/orlow light-tolerance nucleic acid can have a nucleotide sequence with atleast 80% sequence identity, e.g., 81%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the nucleotide sequence set forth in SEQ ID NO:454or SEQ ID NO:455.

An SD+EODFR and/or low light-tolerance nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:537. Alternatively, anSD+EODFR and/or low light-tolerance nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:537.For example, an SD+EODFR and/or low light-tolerance nucleic acid canhave a nucleotide sequence with at least 80% sequence identity, e.g.,81%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to thenucleotide sequence set forth in SEQ ID NO:537.

An SD+EODFR and/or low light-tolerance nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:568 or SEQ ID NO:569.Alternatively, an SD+EODFR and/or low light-tolerance nucleic acid canbe a variant of the nucleic acid having the nucleotide sequence setforth in SEQ ID NO:568 or SEQ ID NO:569. For example, an SD+EODFR and/orlow light-tolerance nucleic acid can have a nucleotide sequence with atleast 80% sequence identity, e.g., 81%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the nucleotide sequence set forth in SEQ ID NO:568or SEQ ID NO:569.

An SD+EODFR and/or low light-tolerance nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:604 or SEQ ID NO:605.Alternatively, an SD+EODFR and/or low light-tolerance nucleic acid canbe a variant of the nucleic acid having the nucleotide sequence setforth in SEQ ID NO:604 or SEQ ID NO:605. For example, an SD+EODFR and/orlow light-tolerance nucleic acid can have a nucleotide sequence with atleast 80% sequence identity, e.g., 81%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the nucleotide sequence set forth in SEQ ID NO:604or SEQ ID NO:605.

An SD+EODFR and/or low light-tolerance nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:632 or SEQ ID NO:633.Alternatively, an SD+EODFR and/or low light-tolerance nucleic acid canbe a variant of the nucleic acid having the nucleotide sequence setforth in SEQ ID NO:632 or SEQ ID NO:633. For example, an SD+EODFR and/orlow light-tolerance nucleic acid can have a nucleotide sequence with atleast 80% sequence identity, e.g., 81%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the nucleotide sequence set forth in SEQ ID NO:632or SEQ ID NO:633.

An SD+EODFR and/or low light-tolerance nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:642 or SEQ ID NO:643.Alternatively, an SD+EODFR and/or low light-tolerance nucleic acid canbe a variant of the nucleic acid having the nucleotide sequence setforth in SEQ ID NO:642 or SEQ ID NO:643. For example, an SD+EODFR and/orlow light-tolerance nucleic acid can have a nucleotide sequence with atleast 80% sequence identity, e.g., 81%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the nucleotide sequence set forth in SEQ ID NO:642or SEQ ID NO:643.

An SD+EODFR and/or low light-tolerance nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:848 or SEQ ID NO:849.Alternatively, an SD+EODFR and/or low light-tolerance nucleic acid canbe a variant of the nucleic acid having the nucleotide sequence setforth in SEQ ID NO:848 or SEQ ID NO:849. For example, an SD+EODFR and/orlow light-tolerance nucleic acid can have a nucleotide sequence with atleast 80% sequence identity, e.g., 81%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the nucleotide sequence set forth in SEQ ID NO:848or SEQ ID NO:849.

An SD+EODFR and/or low light-tolerance nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:905 or SEQ ID NO:906.Alternatively, an SD+EODFR and/or low light-tolerance nucleic acid canbe a variant of the nucleic acid having the nucleotide sequence setforth in SEQ ID NO:905 or SEQ ID NO:906. For example, an SD+EODFR and/orlow light-tolerance nucleic acid can have a nucleotide sequence with atleast 80% sequence identity, e.g., 81%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the nucleotide sequence set forth in SEQ ID NO:905or SEQ ID NO:906.

An SD+EODFR and/or low light-tolerance nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:951 or SEQ ID NO:952.Alternatively, an SD+EODFR and/or low light-tolerance nucleic acid canbe a variant of the nucleic acid having the nucleotide sequence setforth in SEQ ID NO:951 or SEQ ID NO:952. For example, an SD+EODFR and/orlow light-tolerance nucleic acid can have a nucleotide sequence with atleast 80% sequence identity, e.g., 81%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the nucleotide sequence set forth in SEQ ID NO:951or SEQ ID NO:952.

An SD+EODFR and/or low light-tolerance nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:1019, SEQ ID NO:1020, SEQ IDNO:1021, SEQ ID NO:1022, or SEQ ID NO:1023. Alternatively, an SD+EODFRand/or low light-tolerance nucleic acid can be a variant of the nucleicacid having the nucleotide sequence set forth in SEQ ID NO:1019, SEQ IDNO:1020, SEQ ID NO:1021, SEQ ID NO:1022, or SEQ ID NO:1023. For example,an SD+EODFR and/or low light-tolerance nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:1019, SEQ ID NO:1020, SEQ ID NO:1021, SEQ IDNO:1022, or SEQ ID NO:1023.

An SD+EODFR and/or low light-tolerance nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:1045 or SEQ ID NO:1046.Alternatively, an SD+EODFR and/or low light-tolerance nucleic acid canbe a variant of the nucleic acid having the nucleotide sequence setforth in SEQ ID NO:1045 or SEQ ID NO:1046. For example, an SD+EODFRand/or low light-tolerance nucleic acid can have a nucleotide sequencewith at least 80% sequence identity, e.g., 81%, 85%, 90%, 95%, 97%, 98%,or 99% sequence identity, to the nucleotide sequence set forth in SEQ IDNO:1045 or SEQ ID NO:1046.

An SD+EODFR and/or low light-tolerance nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:1150. Alternatively, anSD+EODFR and/or low light-tolerance nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:1150. For example, an SD+EODFR and/or low light-tolerance nucleic acidcan have a nucleotide sequence with at least 80% sequence identity,e.g., 81%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to thenucleotide sequence set forth in SEQ ID NO:1150.

An SD+EODFR and/or low light-tolerance nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:1275 or SEQ ID NO:1276.Alternatively, an SD+EODFR and/or low light-tolerance nucleic acid canbe a variant of the nucleic acid having the nucleotide sequence setforth in SEQ ID NO:1275 or SEQ ID NO:1276. For example, an SD+EODFRand/or low light-tolerance nucleic acid can have a nucleotide sequencewith at least 80% sequence identity, e.g., 81%, 85%, 90%, 95%, 97%, 98%,or 99% sequence identity, to the nucleotide sequence set forth in SEQ IDNO:1275 or SEQ ID NO:1276.

An SD+EODFR and/or low light-tolerance nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:1345 or SEQ ID NO:1346.Alternatively, an SD+EODFR and/or low light-tolerance nucleic acid canbe a variant of the nucleic acid having the nucleotide sequence setforth in SEQ ID NO:1345 or SEQ ID NO:1346. For example, an SD+EODFRand/or low light-tolerance nucleic acid can have a nucleotide sequencewith at least 80% sequence identity, e.g., 81%, 85%, 90%, 95%, 97%, 98%,or 99% sequence identity, to the nucleotide sequence set forth in SEQ IDNO:1345 or SEQ ID NO:1346.

An SD+EODFR and/or low light-tolerance nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:1453, SEQ ID NO:1454, SEQ IDNO:1455, or SEQ ID NO:1456. Alternatively, an SD+EODFR and/or lowlight-tolerance nucleic acid can be a variant of the nucleic acid havingthe nucleotide sequence set forth in SEQ ID NO:1453, SEQ ID NO:1454, SEQID NO:1455, or SEQ ID NO:1456. For example, an SD+EODFR and/or lowlight-tolerance nucleic acid can have a nucleotide sequence with atleast 80% sequence identity, e.g., 81%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the nucleotide sequence set forth in SEQ IDNO:1453, SEQ ID NO:1454, SEQ ID NO:1455, or SEQ ID NO:1456.

An SD+EODFR and/or low light-tolerance nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:1495 or SEQ ID NO:1496.Alternatively, an SD+EODFR and/or low light-tolerance nucleic acid canbe a variant of the nucleic acid having the nucleotide sequence setforth in SEQ ID NO:1495 or SEQ ID NO:1496. For example, an SD+EODFRand/or low light-tolerance nucleic acid can have a nucleotide sequencewith at least 80% sequence identity, e.g., 81%, 85%, 90%, 95%, 97%, 98%,or 99% sequence identity, to the nucleotide sequence set forth in SEQ IDNO:1495 or SEQ ID NO:1496.

An SD+EODFR and/or low light-tolerance nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:1537, SEQ ID NO:1538, or SEQID NO:1539. Alternatively, an SD+EODFR and/or low light-tolerancenucleic acid can be a variant of the nucleic acid having the nucleotidesequence set forth in SEQ ID NO:1537, SEQ ID NO:1538, or SEQ ID NO:1539.For example, an SD+EODFR and/or low light-tolerance nucleic acid canhave a nucleotide sequence with at least 80% sequence identity, e.g.,81%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to thenucleotide sequence set forth in SEQ ID NO:1537, SEQ ID NO:1538, or SEQID NO:1539.

An SD+EODFR and/or low light-tolerance nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:1585 or SEQ ID NO:1586.Alternatively, an SD+EODFR and/or low light-tolerance nucleic acid canbe a variant of the nucleic acid having the nucleotide sequence setforth in SEQ ID NO:1585 or SEQ ID NO:1586. For example, an SD+EODFRand/or low light-tolerance nucleic acid can have a nucleotide sequencewith at least 80% sequence identity, e.g., 81%, 85%, 90%, 95%, 97%, 98%,or 99% sequence identity, to the nucleotide sequence set forth in SEQ IDNO:1585 or SEQ ID NO:1586.

An SD+EODFR and/or low light-tolerance nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:1626, SEQ ID NO:1627, SEQ IDNO:1628, or SEQ ID NO:1629. Alternatively, an SD+EODFR and/or lowlight-tolerance nucleic acid can be a variant of the nucleic acid havingthe nucleotide sequence set forth in SEQ ID NO:1626, SEQ ID NO:1627, SEQID NO:1628, or SEQ ID NO:1629. For example, an SD+EODFR and/or lowlight-tolerance nucleic acid can have a nucleotide sequence with atleast 80% sequence identity, e.g., 81%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the nucleotide sequence set forth in SEQ IDNO:1626, SEQ ID NO:1627, SEQ ID NO:1628, or SEQ ID NO:1629.

An SD+EODFR and/or low light-tolerance nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:1633 or SEQ ID NO:1634.Alternatively, an SD+EODFR and/or low light-tolerance nucleic acid canbe a variant of the nucleic acid having the nucleotide sequence setforth in SEQ ID NO:1633 or SEQ ID NO:1634. For example, an SD+EODFRand/or low light-tolerance nucleic acid can have a nucleotide sequencewith at least 80% sequence identity, e.g., 81%, 85%, 90%, 95%, 97%, 98%,or 99% sequence identity, to the nucleotide sequence set forth in SEQ IDNO:1633 or SEQ ID NO:1634.

B. Nucleic Acids Encoding Red Light Specific Response PathwayPolypeptides

Nucleic acids encoding red light specific response pathway polypeptidesare described herein. Such nucleic acids include SEQ ID NOs: 454, 455,461, 463, 465, 467, 469, 471, 473, 476, 490, 492, 500, 502, 504, 506,513, 517, 519, 951, 952, 954, 956, 958, 960, 962, 964, 968, 970, 972,974, 976, 978, 980, 982, 984, 986, 988, 990, 992, 994, 996, 998, 1000,1002, 1004, 1006, 1008, 1010, 1012, 1017, 1537, 1538, 1539, 1542, 1544,1546, 1548, 1550, 1552, 1560, 1562, 1569, 1571, 1573, 1575, 1577, 1579,1581, 1583, 1660, 1662, 1664, 1666, 1668, 1670, 1672, 1674, 1676, 1779,1781, 1783, 1785, 1787, 1789, 1791, 1793, 1795, 1797, 1799, 1801, 1803,1841, and 2267 as described in more detail below. A nucleic acid alsocan be a fragment that is at least 40% (e.g., at least 45, 50, 55, 60,65, 70, 75, 80, 85, 90, 95, or 99%) of the length of the full-lengthnucleic acid set forth in SEQ ID NOs: 454, 455, 461, 463, 465, 467, 469,471, 473, 476, 490, 492, 500, 502, 504, 506, 513, 517, 519, 951, 952,954, 956, 958, 960, 962, 964, 968, 970, 972, 974, 976, 978, 980, 982,984, 986, 988, 990, 992, 994, 996, 998, 1000, 1002, 1004, 1006, 1008,1010, 1012, 1017, 1537, 1538, 1539, 1542, 1544, 1546, 1548, 1550, 1552,1560, 1562, 1569, 1571, 1573, 1575, 1577, 1579, 1581, 1583, 1660, 1662,1664, 1666, 1668, 1670, 1672, 1674, 1676, 1779, 1781, 1783, 1785, 1787,1789, 1791, 1793, 1795, 1797, 1799, 1801, 1803, 1841, and 2267.

A red light specific response pathway nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:454 or SEQ ID NO:455.Alternatively, a red light specific response pathway nucleic acid can bea variant of the nucleic acid having the nucleotide sequence set forthin SEQ ID NO:454 or SEQ ID NO:455. For example, a red light specificresponse pathway nucleic acid can have a nucleotide sequence with atleast 80% sequence identity, e.g., 81%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the nucleotide sequence set forth in SEQ ID NO:454or SEQ ID NO:455.

A red light specific response pathway nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:951 or SEQ ID NO:952.Alternatively, a red light specific response pathway nucleic acid can bea variant of the nucleic acid having the nucleotide sequence set forthin SEQ ID NO:951 or SEQ ID NO:952. For example, a red light specificresponse pathway nucleic acid can have a nucleotide sequence with atleast 80% sequence identity, e.g., 81%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the nucleotide sequence set forth in SEQ ID NO:951or SEQ ID NO:952.

A red light specific response pathway nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:1537, SEQ ID NO:1538, or SEQID NO:1539. Alternatively, a red light specific response pathway nucleicacid can be a variant of the nucleic acid having the nucleotide sequenceset forth in SEQ ID NO:1537, SEQ ID NO:1538, or SEQ ID NO:1539. Forexample, a red light specific response pathway nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:1537, SEQ ID NO:1538, or SEQ ID NO:1539.

Isolated nucleic acid molecules can be produced by standard techniques.For example, polymerase chain reaction (PCR) techniques can be used toobtain an isolated nucleic acid containing a nucleotide sequencedescribed herein. PCR can be used to amplify specific sequences from DNAas well as RNA, including sequences from total genomic DNA or totalcellular RNA. Various PCR methods are described, for example, in PCRPrimer A Laboratory Manual, Dieffenbach and Dveksler, eds., Cold SpringHarbor Laboratory Press, 1995. Generally, sequence information from theends of the region of interest or beyond is employed to designoligonucleotide primers that are identical or similar in sequence toopposite strands of the template to be amplified. Various PCR strategiesalso are available by which site-specific nucleotide sequencemodifications can be introduced into a template nucleic acid. Isolatednucleic acids also can be chemically synthesized, either as a singlenucleic acid molecule (e.g., using automated DNA synthesis in the 3′ to5′ direction using phosphoramidite technology) or as a series ofoligonucleotides. For example, one or more pairs of longoligonucleotides (e.g., >100 nucleotides) can be synthesized thatcontain the desired sequence, with each pair containing a short segmentof complementarity (e.g., about 15 nucleotides) such that a duplex isformed when the oligonucleotide pair is annealed. DNA polymerase is usedto extend the oligonucleotides, resulting in a single, double-strandednucleic acid molecule per oligonucleotide pair, which then can beligated into a vector. Isolated nucleic acids of the invention also canbe obtained by mutagenesis of, e.g., a naturally occurring DNA.

C. Use of Nucleic Acids to Modulate Expression of PolypeptidesExpression of an SD+EODFR and/or Low Light-Tolerance Polypeptide

A nucleic acid encoding one of the SD+EODFR and/or low light-tolerancepolypeptides described herein can be used to express the polypeptide ina plant species of interest, typically by transforming a plant cell witha nucleic acid having the coding sequence for the polypeptide operablylinked in sense orientation to one or more regulatory regions. It willbe appreciated that because of the degeneracy of the genetic code, anumber of nucleic acids can encode a particular SD+EODFR and/or lowlight-tolerance polypeptide; i.e., for many amino acids, there is morethan one nucleotide triplet that serves as the codon for the amino acid.Thus, codons in the coding sequence for a given SD+EODFR and/or lowlight-tolerance polypeptide can be modified such that optimal expressionin a particular plant species is obtained, using appropriate codon biastables for that species.

In some cases, expression of an SD+EODFR and/or low light-tolerancepolypeptide inhibits one or more functions of an endogenous polypeptide.For example, a nucleic acid that encodes a dominant negative polypeptidecan be used to inhibit protein function. A dominant negative polypeptidetypically is mutated or truncated relative to an endogenous wild typepolypeptide, and its presence in a cell inhibits one or more functionsof the wild type polypeptide in that cell, i.e., the dominant negativepolypeptide is genetically dominant and confers a loss of function. Themechanism by which a dominant negative polypeptide confers such aphenotype can vary but often involves a protein-protein interaction or aprotein-DNA interaction. For example, a dominant negative polypeptidecan be an enzyme that is truncated relative to a native wild typeenzyme, such that the truncated polypeptide retains domains involved inbinding a first protein but lacks domains involved in binding a secondprotein. The truncated polypeptide is thus unable to properly modulatethe activity of the second protein. See, e.g., US 2007/0056058. Asanother example, a point mutation that results in a non-conservativeamino acid substitution in a catalytic domain can result in a dominantnegative polypeptide. See, e.g., US 2005/032221. As another example, adominant negative polypeptide can be a transcription factor that istruncated relative to a native wild type transcription factor, such thatthe truncated polypeptide retains the DNA binding domain(s) but lacksthe activation domain(s). Such a truncated polypeptide can inhibit thewild type transcription factor from binding DNA, thereby inhibitingtranscription activation.

D. Use of Nucleic Acids to Inhibit Expression of a Red Light SpecificResponse Pathway Polypeptide

Polynucleotides and recombinant constructs described herein can be usedto inhibit expression of a red light specific response pathwaypolypeptide in a plant species of interest. See, e.g., Matzke andBirchler, Nature Reviews Genetics, 6:24-35 (2005); Akashi et al., NatureReviews Mol. Cell Biology, 6:413-422 (2005); Mittal, Nature ReviewsGenetics, 5:355-365 (2004); and Nature Reviews RNA interferencecollection, October 2005 at nature.com/reviews/focus/mai. A number ofnucleic acid based methods, including antisense RNA, ribozyme directedRNA cleavage, post-transcriptional gene silencing (PTGS), e.g., RNAinterference (RNAi), and transcriptional gene silencing (TGS) are knownto inhibit gene expression in plants. Suitable polynucleotides includefull-length nucleic acids encoding red light specific response pathwaypolypeptides or fragments of such full-length nucleic acids. In someembodiments, a complement of the full-length nucleic acid or a fragmentthereof can be used. Typically, a fragment is at least 10 nucleotides,e.g., at least 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 30, 35, 40, 50, 80, 100, 200, 500 nucleotides or more.Generally, higher homology can be used to compensate for the use of ashorter sequence.

Antisense technology is one well-known method. In this method, a nucleicacid of a gene to be repressed is cloned and operably linked to aregulatory region and a transcription termination sequence so that theantisense strand of RNA is transcribed. The recombinant construct isthen transformed into plants, as described herein, and the antisensestrand of RNA is produced. The nucleic acid need not be the entiresequence of the gene to be repressed, but typically will besubstantially complementary to at least a portion of the sense strand ofthe gene to be repressed.

In another method, a nucleic acid can be transcribed into a ribozyme, orcatalytic RNA, that affects expression of an mRNA. See, U.S. Pat. No.6,423,885. Ribozymes can be designed to specifically pair with virtuallyany target RNA and cleave the phosphodiester backbone at a specificlocation, thereby functionally inactivating the target RNA. Heterologousnucleic acids can encode ribozymes designed to cleave particular mRNAtranscripts, thus preventing expression of a polypeptide. Hammerheadribozymes are useful for destroying particular mRNAs, although variousribozymes that cleave mRNA at site-specific recognition sequences can beused. Hammerhead ribozymes cleave mRNAs at locations dictated byflanking regions that form complementary base pairs with the targetmRNA. The sole requirement is that the target RNA contains a 5′-UG-3′nucleotide sequence. The construction and production of hammerheadribozymes is known in the art. See, for example, U.S. Pat. No. 5,254,678and WO 02/46449 and references cited therein. Hammerhead ribozymesequences can be embedded in a stable RNA such as a transfer RNA (tRNA)to increase cleavage efficiency in vivo. Perriman et al., Proc. Natl.Acad. Sci. USA, 92(13):6175-6179 (1995); de Feyter and Gaudron, Methodsin Molecular Biology, Vol. 74, Chapter 43, “Expressing Ribozymes inPlants”, Edited by Turner. P. C., Humana Press Inc., Totowa, N.J. RNAendoribonucleases which have been described, such as the one that occursnaturally in Tetrahymena thermophila, can be useful. See, for example,U.S. Pat. Nos. 4,987,071 and 6,423,885.

PTGS, e.g., RNAi, can also be used to inhibit the expression of a gene.For example, a construct can be prepared that includes a sequence thatis transcribed into an RNA that can anneal to itself, e.g., a doublestranded RNA having a stem-loop structure. In some embodiments, onestrand of the stem portion of a double stranded RNA comprises a sequencethat is similar or identical to the sense coding sequence or a fragmentthereof of a red light specific response pathway polypeptide, and thatis from about 10 nucleotides to about 2,500 nucleotides in length. Thelength of the sequence that is similar or identical to the sense codingsequence can be from 10 nucleotides to 500 nucleotides, from 15nucleotides to 300 nucleotides, from 20 nucleotides to 100 nucleotides,or from 25 nucleotides to 100 nucleotides. The other strand of the stemportion of a double stranded RNA comprises a sequence that is similar oridentical to the antisense strand or a fragment thereof of the codingsequence of the red light specific response pathway polypeptide, and canhave a length that is shorter, the same as, or longer than thecorresponding length of the sense sequence. In some cases, one strand ofthe stem portion of a double stranded RNA comprises a sequence that issimilar or identical to the 3′ or 5′ untranslated region, or a fragmentthereof, of an mRNA encoding a red light specific response pathwaypolypeptide, and the other strand of the stem portion of the doublestranded RNA comprises a sequence that is similar or identical to thesequence that is complementary to the 3′ or 5′ untranslated region,respectively, or a fragment thereof, of the mRNA encoding the red lightspecific response pathway polypeptide. In other embodiments, one strandof the stem portion of a double stranded RNA comprises a sequence thatis similar or identical to the sequence of an intron, or a fragmentthereof, in the pre-mRNA encoding a red light specific response pathwaypolypeptide, and the other strand of the stem portion comprises asequence that is similar or identical to the sequence that iscomplementary to the sequence of the intron, or a fragment thereof, inthe pre-mRNA.

The loop portion of a double stranded RNA can be from 3 nucleotides to5,000 nucleotides, e.g., from 3 nucleotides to 25 nucleotides, from 15nucleotides to 1,000 nucleotides, from 20 nucleotides to 500nucleotides, or from 25 nucleotides to 200 nucleotides. The loop portionof the RNA can include an intron or a fragment thereof. A doublestranded RNA can have zero, one, two, three, four, five, six, seven,eight, nine, ten, or more stem-loop structures.

A construct including a sequence that is operably linked to a regulatoryregion and a transcription termination sequence, and that is transcribedinto an RNA that can form a double stranded RNA, is transformed intoplants as described herein. Methods for using RNAi to inhibit theexpression of a gene are known to those of skill in the art. See, e.g.,U.S. Pat. Nos. 5,034,323; 6,326,527; 6,452,067; 6,573,099; 6,753,139;and 6,777,588. See also WO 97/01952; WO 98/53083; WO 99/32619; WO98/36083; and U.S. Patent Publications 20030175965, 20030175783,20040214330, and 20030180945.

Constructs containing regulatory regions operably linked to nucleic acidmolecules in sense orientation can also be used to inhibit theexpression of a gene. The transcription product can be similar oridentical to the sense coding sequence, or a fragment thereof, of a redlight specific response pathway polypeptide. The transcription productalso can be unpolyadenylated, lack a 5′ cap structure, or contain anunspliceable intron. Methods of inhibiting gene expression using afull-length cDNA as well as a partial cDNA sequence are known in theart. See, e.g., U.S. Pat. No. 5,231,020.

In some embodiments, a construct containing a nucleic acid having atleast one strand that is a template for both sense and antisensesequences that are complementary to each other is used to inhibit theexpression of a gene. The sense and antisense sequences can be part of alarger nucleic acid molecule or can be part of separate nucleic acidmolecules having sequences that are not complementary. The sense orantisense sequence can be a sequence that is identical or complementaryto the sequence of an mRNA, the 3′ or 5′ untranslated region of an mRNA,or an intron in a pre-mRNA encoding a red light specific responsepathway polypeptide, or a fragment of such sequences. In someembodiments, the sense or antisense sequence is identical orcomplementary to a sequence of the regulatory region that drivestranscription of the gene encoding a red light specific response pathwaypolypeptide. In each case, the sense sequence is the sequence that iscomplementary to the antisense sequence.

The sense and antisense sequences can be a length greater than about 10nucleotides (e.g., 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,25, 26, 27, 28, 29, 30, or more nucleotides). For example, an antisensesequence can be 21 or 22 nucleotides in length. Typically, the sense andantisense sequences range in length from about 15 nucleotides to about30 nucleotides, e.g., from about 18 nucleotides to about 28 nucleotides,or from about 21 nucleotides to about 25 nucleotides.

In some embodiments, an antisense sequence is a sequence complementaryto an mRNA sequence, or a fragment thereof, encoding a red lightspecific response pathway polypeptide described herein. The sensesequence complementary to the antisense sequence can be a sequencepresent within the mRNA of the red light specific response pathwaypolypeptide. Typically, sense and antisense sequences are designed tocorrespond to a 15-30 nucleotide sequence of a target mRNA such that thelevel of that target mRNA is reduced.

In some embodiments, a construct containing a nucleic acid having atleast one strand that is a template for more than one sense sequence(e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10 or more sense sequences) can be usedto inhibit the expression of a gene. Likewise, a construct containing anucleic acid having at least one strand that is a template for more thanone antisense sequence (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10 or moreantisense sequences) can be used to inhibit the expression of a gene.For example, a construct can contain a nucleic acid having at least onestrand that is a template for two sense sequences and two antisensesequences. The multiple sense sequences can be identical or different,and the multiple antisense sequences can be identical or different. Forexample, a construct can have a nucleic acid having one strand that is atemplate for two identical sense sequences and two identical antisensesequences that are complementary to the two identical sense sequences.Alternatively, an isolated nucleic acid can have one strand that is atemplate for (1) two identical sense sequences 20 nucleotides in length,(2) one antisense sequence that is complementary to the two identicalsense sequences 20 nucleotides in length, (3) a sense sequence 30nucleotides in length, and (4) three identical antisense sequences thatare complementary to the sense sequence 30 nucleotides in length. Theconstructs provided herein can be designed to have a suitablearrangement of sense and antisense sequences. For example, two identicalsense sequences can be followed by two identical antisense sequences orcan be positioned between two identical antisense sequences.

A nucleic acid having at least one strand that is a template for one ormore sense and/or antisense sequences can be operably linked to aregulatory region to drive transcription of an RNA molecule containingthe sense and/or antisense sequence(s). In addition, such a nucleic acidcan be operably linked to a transcription terminator sequence, such asthe terminator of the nopaline synthase (nos) gene. In some cases, tworegulatory regions can direct transcription of two transcripts: one fromthe top strand, and one from the bottom strand. See, for example, Yan etal., Plant Physiol., 141:1508-1518 (2006). The two regulatory regionscan be the same or different. The two transcripts can formdouble-stranded RNA molecules that induce degradation of the target RNA.In some cases, a nucleic acid can be positioned within a T-DNA orplant-derived transfer DNA (P-DNA) such that the left and right T-DNAborder sequences, or the left and right border-like sequences of theP-DNA, flank or are on either side of the nucleic acid. See, US2006/0265788. The nucleic acid sequence between the two regulatoryregions can be from about 15 to about 300 nucleotides in length. In someembodiments, the nucleic acid sequence between the two regulatoryregions is from about 15 to about 200 nucleotides in length, from about15 to about 100 nucleotides in length, from about 15 to about 50nucleotides in length, from about 18 to about 50 nucleotides in length,from about 18 to about 40 nucleotides in length, from about 18 to about30 nucleotides in length, or from about 18 to about 25 nucleotides inlength.

In some nucleic-acid based methods for inhibition of gene expression inplants, a suitable nucleic acid can be a nucleic acid analog. Nucleicacid analogs can be modified at the base moiety, sugar moiety, orphosphate backbone to improve, for example, stability, hybridization, orsolubility of the nucleic acid. Modifications at the base moiety includedeoxyuridine for deoxythymidine, and 5-methyl-2′-deoxycytidine and5-bromo-2′-deoxycytidine for deoxycytidine. Modifications of the sugarmoiety include modification of the 2′ hydroxyl of the ribose sugar toform 2′-O-methyl or 2′-O-allyl sugars. The deoxyribose phosphatebackbone can be modified to produce morpholino nucleic acids, in whicheach base moiety is linked to a six-membered morpholino ring, or peptidenucleic acids, in which the deoxyphosphate backbone is replaced by apseudopeptide backbone and the four bases are retained. See, forexample, Summerton and Weller, 1997. Antisense Nucleic Acid Drug Dev.,7:187-195; Hyrup el al., Bloorgan. Med. Chem., 4:5-23 (1996). Inaddition, the deoxyphosphate backbone can be replaced with, for example,a phosphorothioate or phosphorodithioate backbone, a phosphoroamidite,or an alkyl phosphotriester backbone.

E. Constructs/Vectors

Recombinant constructs provided herein can be used to transform plantsor plant cells in order to modulate SD+EODFR,low light tolerance, and/orred light specific response pathways. A recombinant nucleic acidconstruct can comprise a nucleic acid encoding an SD+EODFR and/or lowlight-tolerance polypeptide as described herein, operably linked to aregulatory region suitable for expressing the SD+EODFR and/or lowlight-tolerance polypeptide in the plant or cell. Thus, a nucleic acidcan comprise a coding sequence that encodes any of the SD+EODFR and/orlow light-tolerance polypeptides as set forth in SEQ ID NOs:3, 5, 7, 9,10, 12, 14, 16, 18, 20, 22, 24, 25, 26, 28, 30, 32, 34, 36, 38, 40, 42,44, 46, 48, 49, 51, 53, 55, 57, 59, 60, 61, 62, 63, 65, 67, 70, 72, 74,76, 78, 80, 82, 84, 86, 88, 89, 90, 91, 93, 95, 96, 97, 98, 99, 100,101, 102, 103, 105, 107, 109, 111, 113, 115, 116, 117, 118, 119, 120,121, 122, 124, 126, 129, 130, 131, 132, 133, 135, 137, 139, 141, 143,145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171,173, 175, 177, 179, 181, 183, 185, 187, 188, 189, 191, 193, 195, 197,199, 201, 203, 205, 207, 209, 211, 213, 215, 217, 219, 221, 223, 225,227, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 241, 243,245, 247, 249, 251, 253, 255, 257, 259, 261, 262, 264, 266, 268, 270,271, 273, 275, 277, 279, 281, 283, 285, 287, 289, 291, 292, 293, 294,295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 306, 308, 310, 312,314, 317, 319, 321, 323, 325, 327, 329, 330, 331, 332, 334, 337, 339,341, 343, 344, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 357,359, 361, 362, 364, 365, 366, 367, 368, 370, 372, 374, 376, 378, 379,381, 383, 385, 387, 389, 391, 393, 395, 397, 399, 401, 403, 405, 407,409, 411, 413, 415, 417, 419, 421, 423, 425, 427, 429, 431, 433, 435,437, 439, 441, 443, 445, 447, 449, 451, 453, 456, 457, 458, 459, 460,462, 464, 466, 468, 470, 472, 474, 475, 477, 478, 479, 480, 481, 482,483, 484, 485, 486, 487, 488, 489, 491, 493, 494, 495, 496, 497, 498,499, 501, 503, 505, 507, 508, 509, 510, 511, 512, 514, 515, 516, 518,520, 521, 522, 523, 524, 525, 526, 527, 528, 529, 530, 531, 532, 533,534, 535, 536, 538, 539, 541, 542, 543, 544, 545, 546, 547, 548, 549,550, 552, 554, 555, 556, 557, 558, 559, 560, 561, 562, 563, 564, 565,567, 570, 572, 574, 576, 578, 579, 580, 582, 584, 586, 588, 590, 592,594, 596, 598, 600, 601, 603, 606, 607, 608, 609, 611, 613, 615, 616,617, 618, 620, 621, 622, 624, 625, 626, 628, 629, 631, 634, 636, 637,638, 639, 641, 644, 645, 647, 649, 651, 653, 655, 657, 659, 661, 663,665, 667, 669, 671, 673, 675, 676, 678, 680, 682, 684, 686, 688, 690,692, 694, 695, 697, 699, 701, 702, 704, 706, 708, 709, 711, 712, 713,714, 716, 718, 720, 721, 723, 725, 726, 728, 730, 732, 734, 736, 738,740, 741, 742, 743, 744, 745, 747, 749, 750, 751, 753, 755, 757, 759,761, 762, 763, 764, 765, 767, 769, 771, 773, 774, 776, 778, 779, 780,782, 783, 784, 786, 788, 790, 792, 794, 795, 796, 797, 798, 799, 800,801, 802, 803, 804, 805, 806, 807, 808, 809, 810, 811, 812, 813, 814,815, 816, 817, 818, 819, 820, 821, 822, 823, 824, 826, 827, 829, 830,831, 832, 833, 834, 835, 837, 838, 839, 840, 841, 843, 845, 847, 850,851, 853, 855, 857, 859, 861, 862, 863, 864, 865, 866, 868, 870, 872,874, 876, 877, 879, 881, 883, 885, 887, 889, 891, 893, 895, 897, 898,900, 902, 904, 907, 909, 911, 913, 915, 917, 919, 920, 922, 923, 924,926, 928, 929, 930, 931, 932, 934, 936, 937, 938, 939, 940, 941, 943,945, 947, 948, 949, 950, 953, 955, 957, 959, 961, 963, 965, 966, 967,969, 971, 973, 975, 977, 979, 981, 983, 985, 987, 989, 991, 993, 995,997, 999, 1001, 1003, 1005, 1007, 1009, 1011, 1013, 1014, 1015, 1016,1018, 1024, 1025, 1027, 1029, 1030, 1032, 1033, 1035, 1037, 1039, 1040,1042, 1043, 1044, 1047, 1049, 1051, 1053, 1055, 1057, 1059, 1061, 1063,1065, 1067, 1068, 1069, 1071, 1072, 1073, 1074, 1075, 1077, 1078, 1080,1081, 1083, 1085, 1087, 1089, 1091, 1093, 1095, 1097, 1098, 1099, 1100,1101, 1103, 1105, 1107, 1109, 1111, 1113, 1115, 1117, 1119, 1121, 1123,1125, 1127, 1129, 1131, 1133, 1134, 1135, 1136, 1137, 1138, 1139, 1141,1143, 1145, 1147, 1149, 1151, 1153, 1155, 1157, 1159, 1160, 1161, 1162,1164, 1166, 1168, 1170, 1172, 1174, 1176, 1178, 1180, 1182, 1184, 1186,1188, 1190, 1192, 1194, 1196, 1198, 1199, 1200, 1201, 1202, 1203, 1204,1206, 1208, 1209, 1211, 1213, 1214, 1215, 1216, 1217, 1219, 1221, 1223,1225, 1227, 1229, 1230, 1232, 1234, 1236, 1238, 1240, 1242, 1244, 1246,1248, 1250, 1252, 1254, 1255, 1256, 1257, 1258, 1259, 1260, 1261, 1262,1263, 1264, 1266, 1268, 1270, 1272, 1274, 1277, 1279, 1281, 1283, 1285,1287, 1289, 1291, 1293, 1294, 1295, 1297, 1298, 1299, 1301, 1303, 1305,1307, 1309, 1311, 1313, 1315, 1317, 1319, 1321, 1322, 1323, 1324, 1325,1326, 1327, 1328, 1329, 1330, 1331, 1332, 1334, 1336, 1338, 1340, 1342,1344, 1347, 1349, 1351, 1352, 1353, 1355, 1357, 1358, 1360, 1362, 1364,1366, 1367, 1368, 1370, 1372, 1374, 1375, 1377, 1379, 1381, 1383, 1385,1387, 1389, 1391, 1393, 1395, 1397, 1399, 1401, 1402, 1404, 1406, 1408,1410, 1411, 1412, 1413, 1414, 1415, 1417, 1419, 1421, 1422, 1423, 1424,1425, 1426, 1427, 1429, 1430, 1431, 1433, 1434, 1435, 1436, 1438, 1439,1440, 1442, 1444, 1446, 1448, 1450, 1452, 1457, 1458, 1460, 1462, 1464,1466, 1467, 1468, 1469, 1471, 1473, 1475, 1477, 1478, 1479, 1480, 1481,1482, 1483, 1484, 1485, 1486, 1488, 1490, 1492, 1494, 1497, 1499, 1501,1502, 1503, 1504, 1505, 1506, 1508, 1510, 1511, 1512, 1513, 1514, 1515,1516, 1518, 1519, 1520, 1521, 1522, 1523, 1524, 1525, 1527, 1528, 1529,1531, 1532, 1533, 1534, 1535, 1536, 1540, 1541, 1543, 1545, 1547, 1549,1551, 1553, 1554, 1555, 1556, 1557, 1558, 1559, 1561, 1563, 1564, 1565,1566, 1567, 1568, 1570, 1572, 1574, 1576, 1578, 1580, 1582, 1584, 1587,1589, 1591, 1593, 1594, 1596, 1597, 1598, 1599, 1600, 1601, 1602, 1603,1604, 1605, 1606, 1607, 1609, 1611, 1612, 1613, 1614, 1615, 1616, 1617,1618, 1619, 1620, 1621, 1623, 1625, 1630, 1631, 1632, 1635, 1637, 1639,1641, 1642, 1643, 1644, 1646, 1648, 1650, 1651, 1652, 1653, 1654, 1655,1657, 1659, 1661, 1663, 1665, 1667, 1669, 1671, 1673, 1675, 1677, 1679,1681, 1682, 1684, 1686, 1688, 1690, 1692, 1694, 1696, 1698, 1699, 1700,1701, 1702, 1703, 1704, 1705, 1707, 1709, 1711, 1713, 1715, 1717, 1719,1720, 1721, 1722, 1723, 1725, 1727, 1729, 1730, 1732, 1734, 1736, 1738,1739, 1740, 1741, 1742, 1743, 1744, 1745, 1746, 1748, 1750, 1751, 1752,1754, 1756, 1758, 1760, 1762, 1764, 1766, 1767, 1768, 1769, 1770, 1771,1772, 1773, 1774, 1775, 1776, 1777, 1778, 1780, 1782, 1784, 1786, 1788,1790, 1792, 1794, 1796, 1798, 1800, 1802, 1804, 1805, 1806, 1807, 1808,1809, 1810, 1811, 1812, 1813, 1814, 1815, 1816, 1817, 1818, 1819, 1820,1821, 1822, 1823, 1824, 1825, 1826, 1827, 1828, 1829, 1830, 1831, 1832,1833, 1834, 1835, 1836, 1837, 1838, 1839, 1840, 1842, 1843, 1844, 1845,1846, 1847, 1848, 1850, 1852, 1854, 1856, 1858, 1859, 1860, 1861, 1862,1863, 1864, 1865, 1866, 1867, 1869, 1870, 1871, 1873, 1875, 1877, 1879,1881, 1883, 1885, 1887, 1889, 1891, 1893, 1895, 1897, 1899, 1901, 1903,1905, 1907, 1909, 1911, 1913, 1915, 1917, 1919, 1921, 1923, 1925, 1927,1929, 1931, 1933, 1935, 1937, 1939, 1941, 1943, 1945, 1947, 1949, 1951,1953, 1955, 1957, 1959, 1961, 1963, 1965, 1967, 1969, 1971, 1973, 1975,1977, 1979, 1981, 1983, 1985, 1987, 1989, 1991, 1993, 1995, 1997, 1999,2001, 2003, 2005, 2007, 2009, 2011, 2013, 2015, 2017, 2019, 2021, 2023,2025, 2027, 2029, 2030, 2031, 2032, 2033, 2034, 2035, 2036, 2037, 2038,2039, 2040, 2041, 2042, 2043, 2044, 2045, 2046, 2047, 2048, 2049, 2050,2051, 2052, 2053, 2054, 2055, 2056, 2057, 2058, 2059, 2060, 2061, 2062,2063, 2064, 2065, 2066, 2067, 2069, 2070, 2072, 2074, 2076, 2078, 2080,2081, 2083, 2084, 2085, 2087, 2089, 2091, 2093, 2095, 2097, 2099, 2101,2103, 2105, 2107, 2109, 2111, 2113, 2114, 2115, 2116, 2117, 2118, 2119,2120, 2121, 2123, 2125, 2127, 2129, 2131, 2133, 2135, 2136, 2137, 2138,2139, 2140, 2141, 2142, 2143, 2144, 2146, 2148, 2150, 2152, 2154, 2156,2158, 2160, 2162, 2164, 2166, 2168, 2170, 2172, 2174, 2176, 2178, 2180,2182, 2183, 2184, 2185, 2186, 2187, 2188, 2189, 2190, 2191, 2192, 2193,2194, 2195, 2196, 2197, 2198, 2199, 2200, 2201, 2202, 2203, 2204, 2205,2206, 2207, 2208, 2209, 2210, 2211, 2212, 2213, 2214, 2215, 2216, 2217,2218, 2219, 2220, 2221, 2222, 2223, 2224, 2225, 2226, 2227, 2228, 2229,2230, 2231, 2232, 2233, 2234, 2235, 2236, 2237, 2238, 2239, 2240, 2241,2242, 2243, 2244, 2245, 2246, 2247, 2248, 2249, 2250, 2251, 2252, 2253,2254, 2255, 2256, 2257, 2258, 2259, 2260, 2261, 2262, 2263, 2264, 2266,2268, 2269, 2270, 2271, 2272, 2273, 2274, 2275, 2276, 2277, 2278, 2280,2282, 2284, 2286, 2288, 2290, 2292, 2294, 2296, 2298, 2300, 2302, 2304,2306, 2308, 2310, 2312, 2314, 2316, 2318, 2320, 2322, 2323, 2324, 2325,2326, 2327, 2328, 2329, 2330, 2331, 2332, 2333, 2334, 2335, 2336, 2337,2338, 2339, 2340, 2341, 2342, 2343, 2344, 2345, 2346, 2347, 2348, 2350,2352, 2354, 2356, 2358, 2360, 2362, 2364, 2366, 2368, 2370, 2372, 2374,2375, 2376, 2377, 2378, 2379, 2380, 2381. Examples of nucleic acidsencoding SD+EODFR and/or low light-tolerance polypeptides are describedherein. The SD+EODFR and/or low light-tolerance polypeptide encoded by arecombinant nucleic acid can be a native SD+EODFR and/or lowlight-tolerance polypeptide, or can be heterologous to the cell. In somecases, the recombinant construct contains a nucleic acid that inhibitsexpression of an SD+EODFR and/or low light-tolerance polypeptide,operably linked to a regulatory region. Examples of suitable regulatoryregions are described in the section entitled “Regulatory Regions.”

Vectors containing recombinant nucleic acid constructs such as thosedescribed herein also are provided. Suitable vector backbones include,for example, those routinely used in the art such as plasmids, viruses,artificial chromosomes, BACs, YACs, or PACs. Suitable expression vectorsinclude, without limitation, plasmids and viral vectors derived from,for example, bacteriophage, baculoviruses, and retroviruses. Numerousvectors and expression systems are commercially available from suchcorporations as Novagen (Madison. WI), Clontech (Palo Alto, Calif.),Stratagene (La Jolla, Calif.), and Invitrogen/Life Technologies(Carlsbad, Calif.).

The vectors provided herein also can include, for example, origins ofreplication, scaffold attachment regions (SARs), and/or markers. Amarker gene can confer a selectable phenotype on a plant cell. Forexample, a marker can confer biocide resistance, such as resistance toan antibiotic (e.g., kanamycin, G418, bleomycin, or hygromycin), or anherbicide (e.g., glyphosate, chlorsulfuron or phosphinothricin). Inaddition, an expression vector can include a tag sequence designed tofacilitate manipulation or detection (e.g., purification orlocalization) of the expressed polypeptide. Tag sequences, such asluciferase, β-glucuronidase (GUS), green fluorescent protein (GFP),glutathione S-transferase (GST), polyhistidine, c-myc, hemagglutinin, orFlag™ tag (Kodak, New Haven, Conn.) sequences typically are expressed asa fusion with the encoded polypeptide. Such tags can be insertedanywhere within the polypeptide, including at either the carboxyl oramino terminus.

F. Regulatory Regions

The choice of regulatory regions to be included in a recombinantconstruct depends upon several factors, including, but not limited to,efficiency, selectability, inducibility, desired expression level, andcell- or tissue-preferential expression. It is a routine matter for oneof skill in the art to modulate the expression of a coding sequence byappropriately selecting and positioning regulatory regions relative tothe coding sequence. Transcription of a nucleic acid can be modulated ina similar manner.

Some suitable regulatory regions initiate transcription only, orpredominantly, in certain cell types. Methods for identifying andcharacterizing regulatory regions in plant genomic DNA are known,including, for example, those described in the following references:Jordano et al., Plant Cell, 1:855-866 (1989); Bustos et al., Plant Cell,1:839-854 (1989): Green et al., EMBO J., 7:4035-4044 (1988); Meier etal., Plant Cell, 3:309-316 (1991); and Zhang et al., Plant Physiology,110:1069-1079 (1996).

Examples of various classes of regulatory regions are described below.Some of the regulatory regions indicated below as well as additionalregulatory regions are described in more detail in U.S. PatentApplication Ser. Nos. 60/505,689; 60/518,075; 60/544,771; 60/558,869;60/583,691; 60/619,181; 60/637,140; 60/757,544; 60/776,307; 10/957,569;11/058,689; 11/172,703; 11/208,308; 11/274,890; 60/583,609; 60/612,891;11/097,589; 11/233,726; 11/408,791; 11/414,142; 10/950,321; 11/360,017;PCT/US05/011105; PCT/US05/23639; PCT/US05/034308; PCT/US05/034343; andPCT/US06/038236; PCT/US06/040572; and PCT/US07/62762.

For example, the sequences of regulatory regions p326, YP0144, YP0190,p13879, YP0050, p32449, 21876, YP0158, YP0214, YP0380, PT0848, PT0633,YP0128, YP0275, PT0660, PT0683, PT0758, PT0613, PT0672, PT0688, PT0837,YP0092, PT0676, PT0708, YP0396, YP0007, YP0111, YP0103, YP0028, YP0121,YP0008, YP0039, YP0115, YP0119, YP0120, YP0374, YP0101, YP0102, YP0110,YP0117, YP0137, YP0285, YP0212, YP0097, YP0107, YP0088, YP0143, YP0156,PT0650, PT0695, PT0723, PT0838, PT0879, PT0740, PT0535, PT0668, PT0886,PT0585, YP0381, YP0337, PT0710, YP0356, YP0385, YP0384, YP0286, YP0377,PD1367, PT0863, PT0829, PT0665, PT0678, YP0086, YP0188, YP0263, PT0743and YP0096 are set forth in the sequence listing of PCT/US06/040572; thesequence of regulatory region PT0625 is set forth in the sequencelisting of PCT/US05/034343; the sequences of regulatory regions PT0623,YP0388, YP0087, YP0093, YP0108, YP0022 and YP0080 are set forth in thesequence listing of U.S. patent application Ser. No. 11/172,703; thesequence of regulatory region PR0924 is set forth in the sequencelisting of PCT/US07/62762; and the sequences of regulatory regionsp530c10, pOsFIE2-2, pOsMEA, pOsYp102, and pOsYp285 are set forth in thesequence listing of PCT/US06/038236.

It will be appreciated that a regulatory region may meet criteria forone classification based on its activity in one plant species, and yetmeet criteria for a different classification based on its activity inanother plant species.

i. Broadly Expressing Promoters

A promoter can be said to be “broadly expressing” when it promotestranscription in many, but not necessarily all, plant tissues. Forexample, a broadly expressing promoter can promote transcription of anoperably linked sequence in one or more of the shoot, shoot tip (apex),and leaves, but weakly or not at all in tissues such as roots or stems.As another example, a broadly expressing promoter can promotetranscription of an operably linked sequence in one or more of the stem,shoot, shoot tip (apex), and leaves, but can promote transcriptionweakly or not at all in tissues such as reproductive tissues of flowersand developing seeds. Non-limiting examples of broadly expressingpromoters that can be included in the nucleic acid constructs providedherein include the p326, YP0144, YP0190, p13879, YP0050, p32449, 21876,YP0158, YP0214, YP0380, PT0848, and PT0633 promoters. Additionalexamples include the cauliflower mosaic virus (CaMV) 35S promoter, themannopine synthase (MAS) promoter, the 1′ or 2′ promoters derived fromT-DNA of Agrobacterium tumefaciens, the figwort mosaic virus 34Spromoter, actin promoters such as the rice actin promoter, and ubiquitinpromoters such as the maize ubiquitin-1 promoter. In some cases, theCaMV 35S promoter is excluded from the category of broadly expressingpromoters.

ii. Root Promoters

Root-active promoters confer transcription in root tissue, e.g., rootendodermis, root epidermis, or root vascular tissues. In someembodiments, root-active promoters are root-preferential promoters,i.e., confer transcription only or predominantly in root tissue.Root-preferential promoters include the YP0128, YP0275, PT0625, PT0660,PT0683, and PT0758 promoters. Other root-preferential promoters includethe PT0613, PT0672, PT0688, and PT0837 promoters, which drivetranscription primarily in root tissue and to a lesser extent in ovulesand/or seeds. Other examples of root-preferential promoters include theroot-specific subdomains of the CaMV 35S promoter (Lam et al., Proc.Natl. Acad. Sci. USA, 86:7890-7894 (1989)), root cell specific promotersreported by Conkling et al., Plant Physiol., 93:1203-1211 (1990), andthe tobacco RD2 promoter.

iii. Maturing Endosperm Promoters

In some embodiments, promoters that drive transcription in maturingendosperm can be useful. Transcription from a maturing endospermpromoter typically begins after fertilization and occurs primarily inendosperm tissue during seed development and is typically highest duringthe cellularization phase. Most suitable are promoters that are activepredominantly in maturing endosperm, although promoters that are alsoactive in other tissues can sometimes be used. Non-limiting examples ofmaturing endosperm promoters that can be included in the nucleic acidconstructs provided herein include the napin promoter, the Arcelin-5promoter, the phaseolin promoter (Bustos et al., Plant Cell,1(9):839-853 (1989)), the soybean trypsin inhibitor promoter (Riggs etal., Plant Cell, 1(6):609-621 (1989)), the ACP promoter (Baerson et al.,Plant Mol. Biol., 22(2):255-267 (1993)), the stearoyl-ACP desaturasepromoter (Slocombe et al., Plant Physiol., 104(4):167-176 (1994)), thesoybean α′ subunit of β-conglycinin promoter (Chen et al., Proc. Natl.Acad. Sci. USA, 83:8560-8564 (1986)), the oleosin promoter (Hong et al.,Plant Mol. Biol., 34(3):549-555 (1997)), and zein promoters, such as the15 kD zein promoter, the 16 kD zein promoter, 19 kD zein promoter, 22 kDzein promoter and 27 kD zein promoter. Also suitable are the Osgt-1promoter from the rice glutelin-1 gene (Zheng et al., Mol. Cell Biol.,13:5829-5842 (1993)), the beta-amylase promoter, and the barley hordeinpromoter. Other maturing endosperm promoters include the YP0092, PT0676,and PT0708 promoters.

iv. Ovary Tissue Promoters

Promoters that are active in ovary tissues such as the ovule wall andmesocarp can also be useful, e.g., a polygalacturonidase promoter, thebanana TRX promoter, the melon actin promoter, YP0396, and PT0623.Examples of promoters that are active primarily in ovules includeYP0007, YP0111, YP0092, YP0103, YP0028, YP0121, YP0008, YP0039, YP0115,YP0119, YP0120, and YP0374.

v. Embryo Sac/Early Endosperm Promoters

To achieve expression in embryo sac/early endosperm, regulatory regionscan be used that are active in polar nuclei and/or the central cell, orin precursors to polar nuclei, but not in egg cells or precursors to eggcells. Most suitable are promoters that drive expression only orpredominantly in polar nuclei or precursors thereto and/or the centralcell. A pattern of transcription that extends from polar nuclei intoearly endosperm development can also be found with embryo sac/earlyendosperm-preferential promoters, although transcription typicallydecreases significantly in later endosperm development during and afterthe cellularization phase. Expression in the zygote or developing embryotypically is not present with embryo sac/early endosperm promoters.

Promoters that may be suitable include those derived from the followinggenes: Arabidopsis viviparous-1 (see, GenBank No. U93215); Arabidopsisatmycl (see, Urao (1996) Plant Mol. Biol., 32:571-57; Conceicao (1994)Plant, 5:493-505); Arabidopsis FIE (GenBank No. AF129516); ArabidopsisMEA; Arabidopsis FIS2 (GenBank No. AF096096); and FIE 1.1 (U.S. Pat. No.6,906,244). Other promoters that may be suitable include those derivedfrom the following genes: maize MAC1 (see, Sheridan (1996) Genetics,142:1009-1020); maize Cat3 (see, GenBank No. L05934; Abler (1993) PlantMol. Biol., 22:10131-1038). Other promoters include the followingArabidopsis promoters: YP0039, YP0101, YP0102, YP0110, YP0117, YP0119,YP0137, DME, YP0285, and YP0212. Other promoters that may be usefulinclude the following rice promoters: p530c10, pOsFIE2-2, pOsMEA,pOsYp102, and pOsYp285.

vi. Embryo Promoters

Regulatory regions that preferentially drive transcription in zygoticcells following fertilization can provide embryo-preferentialexpression. Most suitable are promoters that preferentially drivetranscription in early stage embryos prior to the heart stage, butexpression in late stage and maturing embryos is also suitable.Embryo-preferential promoters include the barley lipid transfer protein(Ltp1) promoter (Plant Cell Rep (2001) 20:647-654), YP0097, YP0107,YP0088, YP0143, YP0156, PT0650, PT0695, PT0723, PT0838, PT0879, andPT0740.

vii. Photosynthetic Tissue Promoters

Promoters active in photosynthetic tissue confer transcription in greentissues such as leaves and stems. Most suitable are promoters that driveexpression only or predominantly in such tissues. Examples of suchpromoters include the ribulose-1,5-bisphosphate carboxylase (RbcS)promoters such as the RbcS promoter from eastern larch (Larix laricina),the pine cab6 promoter (Yamamoto et al., Plant Cell Physiol., 35:773-778(1994)), the Cab-1 promoter from wheat (Fejes et al., Plant Mol. Biol.,15:921-932 (1990)), the CAB-1 promoter from spinach (Lubberstedt et al.,Plant Physiol., 104:997-1006 (1994)), the cab1R promoter from rice (Luanet al., Plant Cell, 4:971-981 (1992)), the pyruvate orthophosphatedikinase (PPDK) promoter from corn (Matsuoka et al., Proc. Natl. Acad.Sci. USA, 90:9586-9590 (1993)), the tobacco Lhcb1*2 promoter (Cerdan etal., Plant Mol. Biol., 33:245-255 (1997)), the Arabidopsis thaliana SUC2sucrose-H+ symporter promoter (Truemit et al., Planta, 196:564-570(1995)), and thylakoid membrane protein promoters from spinach (psaD,psaF, psaE, PC, FNR, atpC, atpD, cab, rbcS). Other photosynthetic tissuepromoters include PT0535, PT0668, PT0886, YP0144, YP0380 and PT0585.

viii. Vascular Tissue Promoters

Examples of promoters that have high or preferential activity invascular bundles include YP0087, YP0093, YP0108, YP0022, and YP0080.Other vascular tissue-preferential promoters include the glycine-richcell wall protein GRP 1.8 promoter (Keller and Baumgartner, Plant Cell,3(10):1051-1061 (1991)), the Commelina yellow mottle virus (CoYMV)promoter (Medberry et al., Plant Cell, 4(2):185-192 (1992)), and therice tungro bacilliform virus (RTBV) promoter (Dai et al., Proc. Natl.Acad. Sci. USA, 101(2):687-692 (2004)).

ix. Inducible Promoters

Inducible promoters confer transcription in response to external stimulisuch as chemical agents or environmental stimuli. For example, induciblepromoters can confer transcription in response to hormones such asgiberellic acid or ethylene, or in response to light or drought.Examples of drought-inducible promoters include YP0380, PT0848, YP0381,YP0337, PT0633, YP0374, PT0710, YP0356, YP0385, YP0396, YP0388, YP0384,PT0688, YP0286, YP0377, PD1367, and PD0901. Examples ofnitrogen-inducible promoters include PT0863, PT0829, PT0665, and PT0886.Examples of shade-inducible promoters include PR0924 and PT0678. Anexample of a promoter induced by salt is rd29A (Kasuga et al. (1999)Nature Biotech 17: 287-291).

x. Basal Promoters

A basal promoter is the minimal sequence necessary for assembly of atranscription complex required for transcription initiation. Basalpromoters frequently include a “TATA box” element that may be locatedbetween about 15 and about 35 nucleotides upstream from the site oftranscription initiation. Basal promoters also may include a “CCAAT box”element (typically the sequence CCAAT) and/or a GGGCG sequence, whichcan be located between about 40 and about 200 nucleotides, typicallyabout 60 to about 120 nucleotides, upstream from the transcription startsite.

xi. Other Promoters

Other classes of promoters include, but are not limited to,shoot-preferential, callus-preferential, trichome cell-preferential,guard cell-preferential such as PT0678, tuber-preferential, parenchymacell-preferential, and senescence-preferential promoters. Promotersdesignated YP0086, YP0188, YP0263, PT0758. PT0743, PT0829, YP0119, andYP0096, as described in the above-referenced patent applications, mayalso be useful.

xii. Other Regulatory Regions

A 5′ untranslated region (UTR) can be included in nucleic acidconstructs described herein. A 5′ UTR is transcribed, but is nottranslated, and lies between the start site of the transcript and thetranslation initiation codon and may include the +1 nucleotide. A 3′ UTRcan be positioned between the translation termination codon and the endof the transcript. UTRs can have particular functions such as increasingmRNA stability or attenuating translation. Examples of 3′ UTRs include,but are not limited to, polyadenylation signals and transcriptiontermination sequences, e.g., a nopaline synthase termination sequence.

It will be understood that more than one regulatory region may bepresent in a recombinant polynucleotide, e.g., introns, enhancers,upstream activation regions, transcription terminators, and inducibleelements. Thus, for example, more than one regulatory region can beoperably linked to the sequence of a polynucleotide encoding an SD+EODFRand/or low light-tolerance polypeptide.

Regulatory regions, such as promoters for endogenous genes, can beobtained by chemical synthesis or by subcloning from a genomic DNA thatincludes such a regulatory region. A nucleic acid comprising such aregulatory region can also include flanking sequences that containrestriction enzyme sites that facilitate subsequent manipulation.

IV. TRANSGENIC PLANTS AND PLANT CELLS A. Transformation

The invention also features transgenic plant cells and plants comprisingat least one recombinant nucleic acid construct described herein. Aplant or plant cell can be transformed by having a construct integratedinto its genome, i.e., can be stably transformed. Stably transformedcells typically retain the introduced nucleic acid with each celldivision. A plant or plant cell can also be transiently transformed suchthat the construct is not integrated into its genome. Transientlytransformed cells typically lose all or some portion of the introducednucleic acid construct with each cell division such that the introducednucleic acid cannot be detected in daughter cells after a sufficientnumber of cell divisions. Both transiently transformed and stablytransformed transgenic plants and plant cells can be useful in themethods described herein.

Transgenic plant cells used in methods described herein can constitutepart or all of a whole plant. Such plants can be grown in a mannersuitable for the species under consideration, either in a growthchamber, a greenhouse, or in a field. Transgenic plants can be bred asdesired for a particular purpose, e.g., to introduce a recombinantnucleic acid into other lines, to transfer a recombinant nucleic acid toother species, or for further selection of other desirable traits.Alternatively, transgenic plants can be propagated vegetatively forthose species amenable to such techniques. As used herein, a transgenicplant also refers to progeny of an initial transgenic plant provided theprogeny inherits the transgene. Seeds produced by a transgenic plant canbe grown and then selfed (or outcrossed and selfed) to obtain seedshomozygous for the nucleic acid construct.

Transgenic plants can be grown in suspension culture, or tissue or organculture. For the purposes of this invention, solid and/or liquid tissueculture techniques can be used. When using solid medium, transgenicplant cells can be placed directly onto the medium or can be placed ontoa filter that is then placed in contact with the medium. When usingliquid medium, transgenic plant cells can be placed onto a flotationdevice, e.g., a porous membrane that contacts the liquid medium. A solidmedium can be, for example, Murashige and Skoog (MS) medium containingagar and a suitable concentration of an auxin, e.g.,2,4-dichlorophenoxyacetic acid (2,4-D), and a suitable concentration ofa cytokinin, e.g., kinetin.

When transiently transformed plant cells are used, a reporter sequenceencoding a reporter polypeptide having a reporter activity can beincluded in the transformation procedure and an assay for reporteractivity or expression can be performed at a suitable time aftertransformation. A suitable time for conducting the assay typically isabout 1-21 days after transformation, e.g., about 1-14 days, about 1-7days, or about 1-3 days. The use of transient assays is particularlyconvenient for rapid analysis in different species, or to confirmexpression of a heterologous SD+EODFR and/or low light-tolerancepolypeptide whose expression has not previously been confirmed inparticular recipient cells.

Techniques for introducing nucleic acids into monocotyledonous anddicotyledonous plants are known in the art, and include, withoutlimitation, Agrobacterium-mediated transformation, viral vector-mediatedtransformation, electroporation and particle gun transformation. e.g.,U.S. Pat. Nos. 5,538,880; 5,204,253; 6,329,571 and 6,013,863. If a cellor cultured tissue is used as the recipient tissue for transformation,plants can be regenerated from transformed cultures if desired, bytechniques known to those skilled in the art.

B. Screening/Selection

A population of transgenic plants can be screened and/or selected forthose members of the population that have a trait or phenotype conferredby expression of the transgene. For example, a population of progeny ofa single transformation event can be screened for those plants having adesired level of expression of an SD+EODFR and/or low light-tolerancepolypeptide or nucleic acid. Physical and biochemical methods can beused to identify expression levels. These include Southern analysis orPCR amplification for detection of a polynucleotide; Northern blots, S1RNase protection, primer-extension, or RT-PCR amplification fordetecting RNA transcripts; enzymatic assays for detecting enzyme orribozyme activity of polypeptides and polynucleotides; and protein gelelectrophoresis, Western blots, immunoprecipitation, and enzyme-linkedimmunoassays to detect polypeptides. Other techniques such as in situhybridization, enzyme staining, and immunostaining also can be used todetect the presence or expression of polypeptides and/orpolynucleotides. Methods for performing all of the referenced techniquesare known. As an alternative, a population of plants comprisingindependent transformation events can be screened for those plantshaving a desired trait, such as a modulated level SD+EODFR and/or lowlight tolerance. Selection and/or screening can be carried out over oneor more generations, and/or in more than one geographic location. Insome cases, transgenic plants can be grown and selected under conditionswhich induce a desired phenotype or are otherwise necessary to produce adesired phenotype in a transgenic plant. In addition, selection and/orscreening can be applied during a particular developmental stage inwhich the phenotype is expected to be exhibited by the plant. Selectionand/or screening can be carried out to choose those transgenic plantshaving a statistically significant difference in SD+EODFR and/or lowlight tolerance level relative to a control plant that lacks thetransgene. Selected or screened transgenic plants have an alteredphenotype as compared to a corresponding control plant, as described inthe “Transgenic Plant Phenotypes” section herein.

C. Plant Species

The polynucleotides and vectors described herein can be used totransform a number of monocotyledonous and dicotyledonous plants andplant cell systems, including species from one of the followingfamilies: Acanthaceae, Alliaceae, Alstroemeriaceae, Amaryilidaceae,Apocynaceae. Arecaceae, Asteraceae, Berberidaceae, Bixaceae,Brassicaceae, Bromeliaceae, Cannabaceae, Caryophyllaceae,Cephalotaxaceae. Chenopodiaceae, Colchicaceae, Cucurbitaceae,Dioscoreaceae, Ephedraceae, Erythroxi-laceae, Euphorbiaceae, Fabaceae,Lamiaceae, Linaceae, Lycopodiaceae, Malvaceae, Melanthiaceae, Musaceae,Myrtaceae, Nyssaceae, Papaveraceae, Pinaceae, Plantaginaceae, Poaceae,Rosaceae, Rubiaceae, Salicaceae, Sapindaceae, Solanaceae, Taxaceae,Theaceae, or Vitaceae.

Suitable species may include members of the genus Abelmoschus, Abies,Acer, Agrostis, Allium, Alstroemeria, Ananas, Andrographis, Andropogon,Artemisia, Arundo, Atropa, Berberis, Beta, Bixa, Brassica, Calendula,Camellia, Camptotheca, Cannabis, Capsicum, Carthamus, Catharanthus,Cephalotaxus, Chrysanthemum, Cinchona, Citrullus, Coffea. Colchicum,Coleus, Cucumis, Cucurbita, Cynodon, Datura, Dianthus, Digitalis,Dioscorea, Elaeis, Ephedra, Erianthus, Erythroxylum, Eucalyptus,Festuca, Fragaria, Galanthus, Glycine, Gossypium, Helianthus, Hevea,Hordeum, Hyoscyamus, Jatropha, Lactuca, Linum, Lolium, Lupinus,Lycopersicon, Lycopodium, Manihot, Medicago, Mentha, Miscanthus, Musa,Nicotiana, Orvza, Panicum, Papaver, Parthenium, Pennisetum, Petunia,Phalaris, Phleum, Pinus, Poa, Poinsettia, Populus, Rauwolfla, Ricinus,Rosa, Saccharum, Salix, Sanguinaria, Scopolia, Secale, Solanum, Sorghum,Spartina, Spinacea, Tanacetum, Taxus, Theobroma, Triticosecale,Triticum, Uniola, Veratrum, Vinca, Vitis, and Zea.

Suitable species include Panicum spp. or hybrids thereof, Sorghum spp.or hybrids thereof, sudangrass, Miscanthus spp. or hybrids thereof,Saccharum spp. or hybrids thereof, Erianthus spp., Populus spp.,Andropogon gerardii (big bluestem), Pennisetum purpureum (elephantgrass) or hybrids thereof (e.g., Pennisetum purpureum x Pennisetumtyphoidum), Phalaris arundinacea (reed canarygrass), Cynodon dactylon(bermudagrass), Festuca arundinacea (tall fescue), Spartina pectinata(prairie cord-grass), Medicago sativa (alfalfa), Arundo donax (giantreed) or hybrids thereof, Secale cereale (rye), Salix spp. (willow),Eucalyptus spp. (eucalyptus), Triticosecale (triticum—wheat X rye) andbamboo.

In some embodiments, a suitable species can be a wild, weedy, orcultivated sorghum species such as, but not limited to, Sorghum almum,Sorghum amplum, Sorghum angustum, Sorghum arundinaceum, Sorghum bicolor(such as bicolor, guinea, caudatum, kafir, and durra), Sorghumbrachypodum, Sorghum bulbosum, Sorghum burmahicum, Sorghum controversum,Sorghum drummondii, Sorghum ecarinatum, Sorghum exstans, Sorghum grande,Sorghum halepense, Sorghum interjectum, Sorghum intrans, Sorghumlaxilorum, Sorghum leiocladum, Sorghum macrospermum, Sorghummatarankense, Sorghum miliaceum, Sorghum nigrum, Sorghum nitidum,Sorghum plumosum, Sorghum propinquum, Sorghum purpureosericeum, Sorghumstipoideum, Sorghum sudanensese, Sorghum timorense, Sorghumtrichocladum, Sorghum versicolor, Sorghum virgatum, Sorghum vulgare, orhybrids such as Sorghum x almum, Sorghum x sudangrass or Sorghum xdrummondii.

Suitable species also include Helianthus annuus (sunflower), Carthamustinctorius (safflower), Jatropha curcas (jatropha), Ricinus communis(castor), Elaeis guineensis (palm), Linum usitatissimum (flax), andBrassica juncea.

Suitable species also include Beta vulgaris (sugarbeet), and Manihotesculenta (cassava).

Suitable species also include Lycopersicon esculentum (tomato). Lactucasaliva (lettuce), Musa paradisiaca (banana), Solanum tuberosum (potato),Brassica oleracea (broccoli, cauliflower, Brussels sprouts), Camelliasinensis (tea), Fragaria ananassa (strawberry), Theobroma cacao (cocoa),Coffea arabica (coffee), Vitis vinygera (grape), Ananas comosus(pineapple), Capsicum annum (hot & sweet pepper), Allium cepa (onion),Cucumis melo (melon), Cucumis sativus (cucumber), Cucurbita maxima(squash), Cucurbita moschata (squash), Spinacea oleracea (spinach),Citrullus lanatus (watermelon), Abelmoschus esculentus (okra), andSolanum melongena (eggplant).

Suitable species also include Papaver somniferum (opium poppy), Papaverorientale, Taxus baccata, Taxus brevifolia, Artemisia annua, Cannabissaliva, Camptotheca acuminate, Catharanthus roseus. Vinca rosea,Cinchona officinalis. Colchicum autumnale, Veratrum californica,Digitalis lanata, Digitalis purpurea, Dioscorea spp., Andrographispaniculata, Atropa belladonna, Datura stomonium, Berberis spp.,Cephalotaxus spp., Ephedra sinica, Ephedra spp., Erythroxylum coca,Galanthus wornorii, Scopolia spp., Lycopodium serratum (=Huperziaserrata), Lycopodium spp., Rauwolfia serpentina, Rauwolfia spp.,Sanguinaria canadensis, Hyoscyamus spp., Calendula officinalis,Chrysanthemum parthenium. Coleus forskohlii, and Tanacetum parthenium.

Suitable species also include Parthenium argentatum (guayule), Heveaspp. (rubber), Mentha spicata (mint), Mentha piperita (mint), Bixaorellana, and Alstroemeria spp.

Suitable species also include Rosa spp. (rose), Dianthus caryophyllus(carnation), Petunia spp. (petunia) and Poinsettia pulcherrima(poinsettia).

Suitable species also include Nicotiana tabacum (tobacco), Lupinus albus(lupin), Uniola paniculata (oats), bentgrass (Agrostis spp.), Populustremuloides (aspen), Pinus spp. (pine), Abies spp. (fir), Acer spp.(maple), Hordeum vulgare (barley), Poa pratensis (bluegrass), Loliumspp. (rycgrass) and Phleum pratense (timothy).

Thus, the methods and compositions can be used over a broad range ofplant species, including species from the dicot genera Brassica,Carthamus, Glycine, Gossypium, Helianthus, Jatropha, Parthenium,Populus, and Ricinus; and the monocot genera Elaeis, Festuca. Hordeum,Lolium, Oryza, Panicum. Pennisetum, Phleum, Poa. Saccharum, Secale,Sorghum, Triticosecale, Triticum, and Zea. In some embodiments, a plantis a member of the species Panicum virgatum (switchgrass). Sorghumbicolor (sorghum, sudangrass), Miscanthus giganteus (miscanthus),Saccharum sp. (energycane), Populus balsamifera (poplar), Zea mays(corn), Glycine max (soybean), Brassica napus (canola), Triticumaestivum (wheat), Gossypium hirsutum (cotton), Oryza sativa (rice),Helianthus annuus (sunflower), Medicago sativa (alfalfa), Beta vulgaris(sugarbeet), or Pennisetum glaucum (pearl millet).

In certain embodiments, the polynucleotides and vectors described hereincan be used to transform a number of monocotyledonous and dicotyledenousplants and plant cell systems, wherein such plants are hybrids ofdifferent species or varieties of a specific species (e.g., Saccharumsp. X Miscanthus sp., Panicum virgatum x Panicum amarum. Panicumvirgatum x Panicum amarulum, and Pennisetum purpureum x Pennisetumtyphoidum).

D. Transgenic Plant Phenotypes

The light in shady environments is enriched in FR wavelengths relativeto the light in non-shady environments. Red wavelengths typically rangefrom a photon irradiance of about 630 nm to a photon irradiance of about700 nm. Far-red wavelengths typically range from a photon irradiance ofabout 700 nm to a photon irradiance of about 750 nm.

In some embodiments, a plant in which expression of an SD+EODFR and/orlow light-tolerance polypeptide is modulated can have increased SD+EODFRand/or low light tolerance. The phenotype of a transgenic plant in whichexpression of an SD+EODFR and/or low light-tolerance polypeptide ismodulated and a corresponding control plant that either lacks thetransgene or does not express the transgene can be evaluated underparticular environmental conditions that are useful for simulatingshade. i.e., Short Day plus End-of-Day Far-Red (SD+EODFR) conditions.SD+EODFR conditions consist of a light period followed by a pulse offar-red-enriched light conditions followed by a 14 hour dark period. Thelight period is from about 9.0 to about 9.6 hours with a red:far-redratio of about 5.5, with the following fluence rates: blue₄₅₀=12μmol/m²/s, red₆₃₃=22 μmol/m²/s, far-red₇₄₀=4 μmol/m²/s, PPFD₄₀₀₋₇₀=55μmol/m²/s. The pulse of far-red-enriched light conditions is from about0.4 to about 1.0 hours with a red:far-red ratio of about 0.14 with thefollowing fluence rates: blue₄₅₀=0.004 μmol/m²/s, red₆₃₃=10 μmol/m²/s,far-red₇₄₀=70 μmoL/m²/s, PPFD₄₀₀₋₇₀₀=8 μmol/m²/s. Sources of lightingequipment appropriate for producing and maintaining SD+EODFR conditionsare known to those in art.

The phenotype of a transgenic plant in which expression of an SD+EODFRand/or low light-tolerance polypeptide is modulated and a correspondingcontrol plant can also be evaluated under conditions of low lightirradiance. Low light conditions are conditions under which a plant isexposed to an irradiance of about 0.01 μmol/m²/s of light to about 20μmol/m²/s of light at room temperature and about 70% relative humidity.For example, conditions under which a plant is exposed to 0.01, 1, 5,10, 15, or 20 μmol/m²/s of light are low light conditions. Sources oflighting and other equipment appropriate for controlling lightconditions are known to those in art.

Low light conditions typically have light of a combination ofwavelengths, such as white light. White light can be supplied, e.g., by32 watt fluorescent bulbs (Sylvania, F032/841/ECO, Danvers, Mass.),providing a red:far-red ratio of 13:1. Red wavelengths typically rangefrom a photon irradiance of about 630 to about 700 nm. Far-redwavelengths typically range from a photon irradiance of about 700 toabout 750 nm.

In some embodiments, the phenotype of a transgenic plant is assayedunder low light conditions in which there is continuous low light duringthe light period of a light/dark cycle. Continuous low light conditionscan be, for example, 16 hours of irradiance with 0.01 to 20 μmol/m²/s oflight alternating with 8 hours of darkness. The phenotype of atransgenic plant is assayed once the plant has been exposed tocontinuous low light conditions during the light period of thelight/dark cycle for seven days.

In some embodiments, the phenotype of a transgenic plant is assayedunder red light conditions in which there is continuous red light.Continuous red light conditions can be, for example, continuousirradiance with about −15 μmol/m²/s of light with a red light to far-redlight ratio (R:FR) of about 80. Continuous red light can be supplied bya LED array that can be used to activate and deactivate the plantphotoreceptor phytochrome (e.g., SNAP-LITE™ Quantum Devices, WI). Thephenotype of a transgenic plant is assayed once the plant has beenexposed to continuous red light conditions for about five days.

In some embodiments, the phenotype of a transgenic plant is assayedunder far-red light conditions in which there is continuous far-redlight. Continuous far-red light conditions can be, for example,continuous irradiance with about 5 μmol/m²/s of light with a R:FR ofabout 0.10. Continuous far-red light can be supplied by a LED array thatcan be used to activate and deactivate the plant photoreceptorphytochrome (e.g., SNAP-LITE™ Quantum Devices, Wis.). The phenotype of atransgenic plant is assayed once the plant has been exposed tocontinuous far-red light conditions for about five days.

In some embodiments, the phenotype of a transgenic plant is assayedunder natural daylight or other broad spectrum light conditions. Naturaldaylight conditions, can be, for example, full sun or other naturalirradiation of green house or field grown transgenic plants. Broadspectrum conditions can be irradiation supplied by a fluorescent lampwith continuous fluence rates of about 12 μmol/m²/s of blue₄₅₀ light, 22μmol/m²/s of red₆₃₃ light, 4 μmol/m²/s far-red₇₄₀ light, andphotosynthetically active radiation (PAR₄₀₀₋₇₀₀) of about 55 μmol/m²/s,with a R:FR of about 5. Other broad spectrum conditions can be, forexample, continuous broadspectrum light during the light period of alight/dark photocycle. In some cases, continuous broad spectrum lightcan be 16 hours of irradiance of about 15 to 55 μmol/m²/s PAR₄₀₀₋₇₀₀,alternating with 8 hours of darkness, with a dark period of 8 hours, forexample. In some cases, continuous broad spectrum light can be 12 hoursof irradiance of about 15 to 55 μmol/m²/s PAR₄₀₀₋₇₀₀, alternating with12 hours of darkness, for example. The phenotype of a transgenic plantis assayed during maturation and/or once the plant has reached maturity.

As compared to a control plant that does not express an SD+EODFR and/orlow light-tolerance polypeptide grown under SD+EODFR conditions or lowlight conditions, a transgenic plant expressing an SD+EODFR and/or lowlight-tolerance polypeptide can exhibit one or more of the followingphenotypes under SD+EODFR conditions or low light conditions: decreasesin extension growth, acceleration in leaf development, decreased apicaldominance, increased chloroplast development, alterations in floweringand seed/fruit production, and an increase in storage organ deposition.

As compared to a control plant that does not overexpress a red specificlight response pathway polypeptide grown under continuous red light orfar-red light conditions, a transgenic plant overexpressing a red lightspecific response pathway polypeptide can exhibit decreases in hypocotyllength under continuous red light or natural daylight conditions, buthas similar hypocotyl length under continuous far-red light or darkconditions.

Typically, a difference (e.g., an increase or a decrease) in amorphological feature in a transgenic plant or cell relative to acontrol plant or cell is considered statistically significant at p≤0.05with an appropriate parametric or non-parametric statistic, e.g.,Chi-square test, Student's t-test, Mann-Whitney test, or F-test. In someembodiments, a difference in the dimensions of any individualmorphological feature is statistically significant at p<0.01, p<0.005,or p<0.001. A statistically significant difference in, for example, amorphological feature in a transgenic plant compared to thecorresponding morphological feature a control plant indicates thatexpression of the recombinant nucleic acid present in the transgenicplant confers the alteration in the morphological feature.

Examples of a decrease in extension growth include, without limitation,decreased petiole length, decreased hypocotyl length, decreasedinternode spacing, and decreased leaf elongation in cereals, whencomparing a transgenic plant expressing an SD+EODFR and/or lowlight-tolerance polypeptide grown under SD+EODFR conditions or low lightconditions to a control plant that does not express an SD+EODFR and/orlow light-tolerance polypeptide grown under SD+EODFR conditions or lowlight conditions. A decrease in extension growth can be a decrease offrom about 0.25% to about 90%, e.g., from about 0.25% to about 15%, fromabout 5% to about 50%, from about 5% to about 10%, from about 25% toabout 50%, from about 1% to about 30%, from about 50% to about 90%, fromabout 20% to about 40%, from about 1% to about 5%, from about 0.5% toabout 2%, from about 15% to about 50%, about 20%, about 25%, about 30%,about 35%, about 40%, about 45%, about 50%, about 55%, about 60%, about65%, about 70%, about 75%, or about 80%.

One suitable phenotype to measure is hypocotyl length. When wild-typeseedlings are grown under SD+EODFR conditions or low light conditions,the hypocotyl length is typically significantly increased relative tothe hypocotyl length found in wild-type seedlings grown under controllight conditions. Thus, seedlings of a transgenic plant and seedlings ofa corresponding control plant that either lacks the transgene or doesnot express the transgene can be grown under SD+EODFR conditions or lowlight conditions and at the appropriate time, hypocotyl lengths fromseedlings of each group can be measured. Under SD+EODFR conditions orlow light conditions, a seedling in which the expression of an SD+EODFRand/or low light-tolerance polypeptide is increased can have astatistically significantly shorter hypocotyl length than a seedling ofa corresponding control plant that either lacks the transgene or doesnot express the transgene. The hypocotyl length can be shorter by atleast 20 percent, e.g., 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75,or 80 percent, as compared to the hypocotyl length in a correspondingcontrol plant that does not express the transgene.

When wild-type seedlings are grown under continuous red-lightconditions, the hypocotyl length is typically significantly decreasedrelative to the hypocotyl length found in wild-type seedlings grownunder continuous far-red light conditions. Thus, seedlings of atransgenic plant and seedlings of a corresponding control plant thateither lacks the transgene or does not express the transgene can begrown under continuous red-light conditions or far-red light conditionsand at the appropriate time, hypocotyl lengths from seedlings of eachgroup can be measured. Under red light conditions, a seedling in whichthe expression of a red light specific response pathway polypeptide isincreased can have a statistically significantly shorter hypocotyllength than a seedling of a corresponding control plant that eitherlacks the transgene or does not express the transgene. The hypocotyllength can be shorter by at least 20 percent, e.g., 20, 25, 30, 35, 40,45, 50, 55, 60, 65, 70, 75, or 80 percent, as compared to the hypocotyllength in a corresponding control plant that does not express thetransgene. Under far-red conditions, a seedling in which the expressionof a red light specific response pathway polypeptide is increased canhave a hypocotyl of similar length to a corresponding control plant thateither lacks the transgene or does not express the transgene.

In contrast, a seedling in which the expression of a red light specificresponse pathway polypeptide is decreased can have a statisticallysignificantly longer hypocotyl length than a seedling of a correspondingcontrol plant that either lacks the transgene or does not express thetransgene. The hypocotyl length can be longer by at least 20 percent,e.g., 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, or 80 percent, ascompared to the hypocotyl length in a corresponding control plant thatdoes not express the transgene. Under far-red conditions, a seedling inwhich the expression of a red light specific response pathwaypolypeptide is decreased can have a hypocotyl of similar length to acorresponding control plant that either lacks the transgene or does notexpress the transgene.

Another suitable phenotype can be overall plant height of mature plants.When wild-type plants are grown under natural light or other broadspectrum light conditions, the plant height at maturity can besignificantly decreased relative to the plant height found in wild-typeplants grown under low light conditions. Thus, the transgenic plant anda corresponding control plant that either lacks the transgene or doesnot express the transgene can be grown under natural light conditions orlow light conditions and at maturity, the height of the plants from eachgroup can be measured. Under natural light or other broad spectrum lightconditions, a mature plant in which the expression of a red lightspecific response pathway polypeptide is decreased can have astatistically significantly taller plant than a mature plant of acorresponding control plant that either lacks the transgene or does notexpress the transgene. The plant height can be taller by at least 20percent, e.g., 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, or 75percent, as compared to the height in a corresponding control plant thatdoes not express the transgene.

Another suitable phenotype can be rate of plant growth. The rate ofplant growth can be determined by measuring differences in fresh weight(T/acre), or differences in subapical cell expansion, over a period oftime, for example. When wild-type plants are grown under natural lightor other broad spectrum light conditions, the rate of plant growth canbe significantly slower relative to the rate of plant growth found inwild-type plants grown under low light conditions. Thus, the transgenicplant and a corresponding control plant that either lacks the transgeneor does not express the transgene can be grown under natural lightconditions or low light conditions and during maturation, the rate ofplant growth for plants from each group can be measured. Under naturallight or other broad spectrum light conditions, a plant in which theexpression of a red light specific response pathway polypeptide isdecreased can have a statistically significantly increased rate of plantgrowth, than a plant of a corresponding control plant that either lacksthe transgene or does not express the transgene. The rate of growth canbe increased by at least least 2 percent, e.g., 2, 3, 4, 5, 6, 7, 8, 9,10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55,60, or more than 60 percent, as compared to the growth rate in acorresponding control plant that does not express the transgene. Anothersuitable phenotype to measure can be dry matter yield of stem parts, orabove ground parts, excluding inflorescence and seed parts of a plant.When wild-type plants are grown under natural light or other broadspectrum light conditions, the dry matter yield can be significantlydecreased relative to the dry matter yield found in wild-type plantsgrown under low light conditions. Thus, the transgenic plant and acorresponding control plant that either lacks the transgene or does notexpress the transgene can be grown under natural light conditions or lowlight conditions and at harvest, the dry matter yield of the plants fromeach group can be measured. Under natural light or other broad spectrumlight conditions, a mature plant in which the expression of a red lightspecific response pathway polypeptide is decreased can have astatistically significantly greater dry matter yield than a mature plantof a corresponding control plant that either lacks the transgene or doesnot express the transgene. Dry matter yield (DMY) yield is calculatedusing the fresh matter weight (FMW) and a measurement of weight percentmoisture (M) in the following equation. DMY=((100−M)/100)*FMW. Forexample, the dry matter yield can be increased by at least 2 percent,e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,20, 25, 30, 35, 40, 45, 50, 55, 60, or more than 60 percent, as comparedto the dry matter yield level in a corresponding control plant that doesnot express the transgene.

Another suitable phenotype to measure is petiole length. When wild-typeseedlings are grown under SD+EODFR conditions or low light conditions,the petiole length is typically significantly increased relative to thepetiole length found in wild-type seedlings grown under control lightconditions. Thus, seedlings of a transgenic plant and seedlings of acorresponding control plant that either lacks the transgene or does notexpress the transgene can be grown under SD+EODFR conditions or lowlight conditions and at the appropriate time, petiole lengths fromseedlings of each group can be measured. Under SD+EODFR conditions orlow light conditions, a seedling in which the expression of an SD+EODFRand/or low light-tolerance polypeptide is increased can have astatistically significantly shorter petiole length than a seedling of acorresponding control plant that either lacks the transgene or does notexpress the transgene. The petiole length can be shorter by at least 20percent, e.g., 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, or 75percent, as compared to the petiole length in a corresponding controlplant that does not express the transgene.

Examples of acceleration in leaf development include, withoutlimitation, increased leaf thickness and increased leaf area growth whencomparing a transgenic plant expressing an SD+EODFR and/or lowlight-tolerance polypeptide grown under SD+EODFR conditions or low lightconditions to a control plant that does not express an SD+EODFR and/orlow light-tolerance polypeptide grown under SD+EODFR conditions or lowlight conditions. Leaf thickness or leaf area growth can be increased byabout 0.25% to about 200% (e.g., about 0.25% to about 2%, about 0.5% toabout 5%, about 0.5% to about 15%, about 2% to about 10%, about 5% toabout 35%, about 10/a to about 25%, about 20% to about 80%, about 50% toabout 200%, about 100% to about 200%, about 100% to about 150%, about5%, about 10%, about 20%, about 35%, about 50%, about 70%, about 90%,about 120%, about 180%, or about 200%) in a transgenic plant expressingan SD+EODFR and/or low light-tolerance polypeptide grown under SD+EODFRconditions or low light conditions as compared to a control plant thatdoes not express an SD+EODFR and/or low light-tolerance polypeptidegrown under SD+EODFR conditions or low light conditions.

Examples of decreased apical dominance include, without limitation,increased branching and increased tillering when comparing a transgenicplant expressing an SD+EODFR and/or low light-tolerance polypeptidegrown under SD+EODFR conditions or low light conditions to a controlplant that does not express an SD+EODFR and/or low light-tolerancepolypeptide grown under SD+EODFR conditions or low light conditions.Branching and tillering can be increased by about 0.25% to about 200%(e.g., about 0.25% to about 2%, about 0.5% to about 5%, about 0.5% toabout 15%, about 2% to about 10%, about 5% to about 35%, about 10% toabout 25%, about 20% to about 80%, about 50% to about 2000% a, about100% to about 200%, about 100% to about 150%, about 5%, about 10%, about20%, about 35%, about 50%, about 70%, about 90%, about 120%, about 180%,or about 200%) in a transgenic plant expressing an SD+EODFR and/or lowlight-tolerance polypeptide grown under SD+EODFR conditions or low lightconditions as compared to a control plant that does not express anSD+EODFR and/or low light-tolerance polypeptide grown under SD+EODFRconditions or low light conditions.

Examples of increased apical dominance include, without limitation,decreased branching and decreased tillering when comparing a transgenicplant in which a red light specific response pathway polypeptide isdown-regulated to a control plant that either lacks the transgene ordoes not express the transgene grown natural light or other broadspectrum light conditions. Branching and tillering can be decreased byabout 0.25% to about 200% (e.g., about 0.25% to about 2%, about 0.5% toabout 5%, about 0.5% to about 15%, about 2% to about 10%, about 5% toabout 35%, about 10¹% to about 25%, about 20% to about 80%, about 50% toabout 200%, about 100% to about 200%, about 100% to about 150%, about5%, about 10%, about 20%, about 35%, about 50%, about 70%, about 90%,about 120%, about 180%, or about 200%) in a transgenic plant in which ared light specific response pathway polypeptide is down-regulated grownunder natural light or other broad spectrum light conditions as comparedto a control plant that either lacks the transgene or does not expressthe transgene grown natural light or other broad spectrum lightconditions.

Examples of increased chloroplast development include, withoutlimitation, increased chlorophyll synthesis and a change in thechlorophyll a:b ratio when comparing a transgenic plant expressing anSD+EODFR and/or low light-tolerance polypeptide grown under SD+EODFRconditions or low light conditions to a control plant that does notexpress an SD+EODFR and/or low light-tolerance polypeptide grown underSD+EODFR conditions or low light conditions. Chlorophyll synthesisand/or the chlorophyll a:b ratio can be about 0.25% to about 200% (e.g.,about 0.25% to about 2%, 0.25% to about 0.5%, about 0.25% to about 1.5%,about 0.5% to about 1%, about 0.5% to about 5%, about 0.5% to about 15%,about 2% to about 10%, about 5% to about 35%, about 10% to about 25%,about 20% to about 80%, about 50% to about 200%, about 100% to about200%, about 100% to about 150%, about 5%, about 10%, about 20%, about35%, about 50%, about 70%, about 90%, about 120%, about 180%, or about200%) greater in a transgenic plant expressing an SD+EODFR and/or lowlight-tolerance polypeptide grown under SD+EODFR conditions or low lightconditions as compared to a control plant that does not express anSD+EODFR and/or low light-tolerance polypeptide grown under SD+EODFRconditions or low light conditions.

Examples of alterations in flowering and seed/fruit production include,without limitation, a decreased rate of flowering, an increase in seedset, and an increase of fruit development when comparing a transgenicplant expressing an SD+EODFR and/or low light-tolerance polypeptidegrown under SD+EODFR conditions or low light conditions to a controlplant that does not express an SD+EODFR and/or low light-tolerancepolypeptide grown under SD+EODFR conditions or low light conditions. Therate of flowering can be a decreased from about 0.25% to about 90%(e.g., from about 0.25% to about 15%, from about 5% to about 50%, fromabout 5% to about 10%, from about 25% to about 50%, from about 1% toabout 30%, from about 50% to about 90%, from about 200% to about 40%,from about 1% to about 5%, from about 0.5% to about 2%, from about 15%to about 50%, about 20%, about 25%, about 30%, about 35%, about 40%,about 45%, about 50%, about 55%, about 60%, about 65%, about 70%, about75%, or about 80%) in a transgenic plant expressing an SD+EODFR and/orlow light-tolerance polypeptide grown under SD+EODFR conditions or lowlight conditions as compared to a control plant that does not express anSD+EODFR and/or low light-tolerance polypeptide grown under SD+EODFRconditions or low light conditions. Seed or fruit weight can beincreased by about 0.25% to about 200% (e.g., about 0.25% to about 2%,about 0.5% to about 5%, about 0.5% to about 15%, about 2% to about 10%,about 5% to about 35%, about 10/a to about 25%, about 20% to about 80%,about 50% to about 200%, about 100% to about 200%, about 100% to about150%, about 5%, about 10%, about 20%, about 35%, about 50%, about 70%,about 90%, about 120%, about 180%, or about 200%) in a transgenic plantexpressing an SD+EODFR and/or low light-tolerance polypeptide grownunder SD+EODFR conditions or low light conditions as compared to acontrol plant that does not express an SD+EODFR and/or lowlight-tolerance polypeptide grown under SD+EODFR conditions or low lightconditions.

The phenotype of a transgenic plant is evaluated relative to a controlplant. A plant is said “not to express” a polypeptide when the plantexhibits less than 10%, e.g., less than 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%,1%, 0.5%, 0.1%, 0.01%, or 0.001%, of the amount of polypeptide or mRNAencoding the polypeptide exhibited by the plant of interest. Expressioncan be evaluated using methods including, for example, RT-PCR, Northernblots, S1 RNase protection, primer extensions, Western blots, proteingel electrophoresis, immunoprecipitation, enzyme-linked immunoassays,chip assays, and mass spectrometry. It should be noted that if apolypeptide is expressed under the control of a tissue-preferential orbroadly expressing promoter, expression can be evaluated in the entireplant or in a selected tissue. Similarly, if a polypeptide is expressedat a particular time, e.g., at a particular time in development or uponinduction, expression can be evaluated selectively at a desired timeperiod.

V. PLANT BREEDING

Genetic polymorphisms are discrete allelic sequence differences in apopulation. Typically, an allele that is present at 1% or greater isconsidered to be a genetic polymorphism. The discovery that polypeptidesdisclosed herein can modulate SD+EODFR and/or low light tolerance isuseful in plant breeding, because genetic polymorphisms exhibiting adegree of linkage with loci for such polypeptides are more likely to becorrelated with variation in SD+EODFR and/or low light tolerance. Forexample, genetic polymorphisms linked to the loci for such polypeptidesare more likely to be useful in marker-assisted breeding programs tocreate lines having SD+EODFR and/or low light tolerance.

Thus, one aspect of the invention includes methods of identifyingwhether one or more genetic polymorphisms are associated with variationin SD+EODFR and/or low light tolerance. Such methods involve determiningwhether genetic polymorphisms in a given population exhibit linkage withthe locus for one of the polypeptides depicted in FIGS. 1-24 and/or afunctional homolog thereof. The correlation is measured betweenvariation in SD+EODFR and/or low light tolerance in plants of thepopulation and the presence of the genetic polymorphism(s) in plants ofthe population, thereby identifying whether or not the geneticpolymorphism(s) are associated with variation for the trait. If thepresence of a particular allele is statistically significantlycorrelated with a desired modulation in SD+EODFR and/or low lighttolerance, the allele is associated with variation for the trait and isuseful as a marker for the trait. If, on the other hand, the presence ofa particular allele is not significantly correlated with the desiredmodulation, the allele is not associated with variation for the traitand is not useful as a marker.

Such methods are applicable to populations containing the naturallyoccurring endogenous polypeptide rather than an exogenous nucleic acidencoding the polypeptide, i.e., populations that are not transgenic forthe exogenous nucleic acid. It will be appreciated, however, thatpopulations suitable for use in the methods may contain a transgene foranother, different trait, e.g., herbicide resistance.

Genetic polymorphisms that are useful in such methods include simplesequence repeats (SSRs, or microsatellites), rapid amplification ofpolymorphic DNA (RAPDs), single nucleotide polymorphisms (SNPs),amplified fragment length polymorphisms (AFLPs) and restriction fragmentlength polymorphisms (RFLPs).

SSR polymorphisms can be identified, for example, by making sequencespecific probes and amplifying template DNA from individuals in thepopulation of interest by PCR. If the probes flank an SSR in thepopulation, PCR products of different sizes will be produced. See, e.g.,U.S. Pat. No. 5,766,847. Alternatively. SSR polymorphisms can beidentified by using PCR product(s) as a probe against Southern blotsfrom different individuals in the population. See, U. H. Refseth et al.,(1997) Electrophoresis 18: 1519. The identification of RFLPs isdiscussed, for example, in Alonso-Blanco et al. (Methods in MolecularBiology, vol. 82, “Arabidopsis Protocols”, pp. 137-146, J. M.Martinez-Zapater and J. Salinas, eds., c. 1998 by Humana Press. Totowa,N.J.); Burr (“Mapping Genes with Recombinant Inbreds”, pp. 249-254, inFreeling, M. and V. Walbot (Ed.), The Maize Handbook, c. 1994 bySpringer-Verlag New York, Inc.: New York, N.Y., USA; Berlin Germany;Burr et al. Genetics (1998) 118: 519; and Gardiner, J. et al., (1993)Genetics 134: 917). The identification of AFLPs is discussed, forexample, in EP 0 534 858 and U.S. Pat. No. 5,878,215.

In some embodiments, the methods are directed to breeding a plant line.Such methods use genetic polymorphisms identified as described above ina marker assisted breeding program to facilitate the development oflines that have a desired alteration in SD+EODFR and/or low lighttolerance. Once a suitable genetic polymorphism is identified as beingassociated with variation for the trait, one or more individual plantsare identified that possess the polymorphic allele correlated with thedesired variation. Those plants are then used in a breeding program tocombine the polymorphic allele with a plurality of other alleles atother loci that are correlated with the desired variation. Techniquessuitable for use in a plant breeding program are known in the art andinclude, without limitation, backcrossing, mass selection, pedigreebreeding, bulk selection, crossing to another population and recurrentselection. These techniques can be used alone or in combination with oneor more other techniques in a breeding program. Thus, each identifiedplants is selfed or crossed a different plant to produce seed which isthen germinated to form progeny plants. At least one such progeny plantis then selfed or crossed with a different plant to form a subsequentprogeny generation. The breeding program can repeat the steps of selfingor outcrossing for an additional 0 to 5 generations as appropriate inorder to achieve the desired uniformity and stability in the resultingplant line, which retains the polymorphic allele. In most breedingprograms, analysis for the particular polymorphic allele will be carriedout in each generation, although analysis can be carried out inalternate generations if desired.

In some cases, selection for other useful traits is also carried out,e.g., selection for fungal resistance or bacterial resistance. Selectionfor such other traits can be carried out before, during or afteridentification of individual plants that possess the desired polymorphicallele.

VI. ARTICLES OF MANUFACTURE

Transgenic plants provided herein have various uses in the agriculturaland energy production industries. For example, transgenic plantsdescribed herein can be used to make animal feed and food products. Suchplants, however, are often particularly useful as a feedstock for energyproduction.

Transgenic plants described herein often produce higher yields of grainand/or biomass per hectare, relative to control plants that lack theexogenous nucleic acid. In some embodiments, such transgenic plantsprovide equivalent or even increased yields of grain and/or biomass perhectare relative to control plants when grown under conditions of lowlight conditions and/or SD+EODFR conditions. Thus, such transgenicplants can be used to provide yield stability under environmentallystressful conditions such as low light conditions and/or SD+EODFRconditions. By providing higher yields under environmentally stressfulconditions such as low light conditions and/or SD+EODFR conditions, thetransgenic plants described herein improve profitability for farmers andprocessors as well as decrease costs to consumers.

Seeds from transgenic plants described herein can be conditioned andbagged in packaging material by means known in the art to form anarticle of manufacture. Packaging material such as paper and cloth arewell known in the art. A package of seed can have a label, e.g., a tagor label secured to the packaging material, a label printed on thepackaging material, or a label inserted within the package, thatdescribes the nature of the seeds therein.

VII. OTHER POLYPEPTIDES, NUCLEIC ACIDS, PLANT CELLS, PLANTS, AND METHODS

In some cases, this document provides methods and materials involved inplant UV-B tolerance. For example, this document provides seeds andplants having cells comprising an exogenous nucleic acid encoding apolypeptide having UV-B tolerance activity as described in U.S. PatentApplication Publication No. 2010-0192261 (U.S. patent application Ser.No. 12/373,134), which is incorporated by reference herein in itsentirety. In some cases, a plant can include a polypeptide or nucleicacid or can be made to include a polypeptide or nucleic acid such thatthe sequence of such a polypeptide or nucleic acid is as set forth inone of the identified sequences of U.S. Patent Application PublicationNo. 2010-0192261 (U.S. patent application Ser. No. 12/373,134) (e.g.,SEQ ID NOs:1-119 of U.S. Patent Application Publication No. 2010-0192261(U.S. patent application Ser. No. 12/373,134)), or is a homolog orortholog thereof as described in U.S. Patent Application Publication No.2010-0192261 (U.S. patent application Ser. No. 12/373,134), or has atleast 80% sequence identity (e.g., at least 80%, 85%, 90%, 95%, 97%,98%, or 99% sequence identity) to an identified sequence of U.S. PatentApplication Publication No. 2010-0192261 (U.S. patent application Ser.No. 12/373,134), as set forth in U.S. Patent Application Publication No.2010-0192261 (U.S. patent application Ser. No. 12/373,134). SEQ IDNOs:1-119 of U.S. Patent Application Publication No. 2010-0192261 (U.S.patent application Ser. No. 12/373,134), together with the identifiedactivities for each of SEQ ID NOs:1-119, the described homologs andorthologs of SEQ ID NOs:1-119 and their associated activities, thesequences having at least 80% sequence identity (e.g., at least 80%,85%, 90%, 95%, 97%, 98%, or 99% sequence identity) to SEQ ID NOs:1-119and their associated activities, the phenotypes of plants containing anyone of SEQ ID NOs:1-119 or the described homologs of SEQ ID NOs:1-119 orthe described orthologs of SEQ ID NOs:1-119 or the described sequenceshaving at least 80% sequence identity to any one of SEQ ID NOs:1-119,and the working examples and data set forth in Examples 1-6 of U.S.Patent Application Publication No. 2010-0192261 (U.S. patent applicationSer. No. 12/373,134) are incorporated by reference herein.

In some cases, this document provides methods and materials involved intolerance of plants to low light conditions. For example, this documentprovides transgenic plants and seeds comprising nucleic acids encodingpolypeptides that confer tolerance to conditions of low light irradianceas described in U.S. Patent Application Publication No. 2010-0205688(U.S. patent application Ser. No. 12/513,086), which is incorporated byreference herein in its entirety. In some cases, a plant can include apolypeptide or nucleic acid or can be made to include a polypeptide ornucleic acid such that the sequence of such a polypeptide or nucleicacid is as set forth in one of the identified sequences of U.S. PatentApplication Publication No. 2010-0205688 (U.S. patent application Ser.No. 12/513,086) (e.g., SEQ ID NOs:1-149 of U.S. Patent ApplicationPublication No. 2010-0205688 (U.S. patent application Ser. No.12/513,086)), or is a homolog or ortholog thereof as described in U.S.Patent Application Publication No. 2010-0205688 (U.S. patent applicationSer. No. 12/513,086), or has at least 80% sequence identity (e.g., atleast 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity) to anidentified sequence of U.S. Patent Application Publication No.2010-0205688 (U.S. patent application Ser. No. 12/513,086), as set forthin U.S. Patent Application Publication No. 2010-0205688 (U.S. patentapplication Ser. No. 12/513,086). SEQ ID NOs:1-149 of U.S. PatentApplication Publication No. 2010-0205688 (U.S. patent application Ser.No. 12/513,086), together with the identified activities for each of SEQID NOs:1-149, the described homologs and orthologs of SEQ ID NOs:1-149and their associated activities, the sequences having at least 80%sequence identity (e.g., at least 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity) to SEQ ID NOs:1-149 and their associated activities,the phenotypes of plants containing any one of SEQ ID NOs:1-149 or thedescribed homologs of SEQ ID NOs:1-149 or the described orthologs of SEQID NOs:1-149 or the described sequences having at least 80% sequenceidentity to any one of SEQ ID NOs:1-149, and the working examples anddata set forth in Examples 1-8 of U.S. Patent Application PublicationNo. 2010-0205688 (U.S. patent application Ser. No. 12/513,086) areincorporated by reference herein.

In some cases, this document provides methods and materials involved inshade tolerance in plants. For example, this document provides plantshaving increased shade tolerance as well as materials and methods formaking plants having increased shade tolerance and plant productsderived from plants having increased shade tolerance as described inU.S. Patent Application Publication No. 2010-0199378 (U.S. patentapplication Ser. No. 12/515,687), which is incorporated by referenceherein in its entirety. In some cases, a plant can include a polypeptideor nucleic acid or can be made to include a polypeptide or nucleic acidsuch that the sequence of such a polypeptide or nucleic acid is as setforth in one of the identified sequences of U.S. Patent ApplicationPublication No. 2010-0199378 (U.S. patent application Ser. No.12/515,687) (e.g., SEQ ID NOs:1-171 of U.S. Patent ApplicationPublication No. 2010-0199378 (U.S. patent application Ser. No.12/515,687)), or is a homolog or ortholog thereof as described in U.S.Patent Application Publication No. 2010-0199378 (U.S. patent applicationSer. No. 12/515,687), or has at least 80% sequence identity (e.g., atleast 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity) to anidentified sequence of U.S. Patent Application Publication No.2010-0199378 (U.S. patent application Ser. No. 12/515,687), as set forthin U.S. Patent Application Publication No. 2010-0199378 (U.S. patentapplication Ser. No. 12/515,687). SEQ ID NOs:1-171 of U.S. PatentApplication Publication No. 2010-0199378 (U.S. patent application Ser.No. 12/515,687), together with the identified activities for each of SEQID NOs:1-171, the described homologs and orthologs of SEQ ID NOs:1-171and their associated activities, the sequences having at least 80%sequence identity (e.g., at least 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity) to SEQ ID NOs:1-171 and their associated activities,the phenotypes of plants containing any one of SEQ ID NOs:1-171 or thedescribed homologs of SEQ ID NOs:1-171 or the described orthologs of SEQID NOs:1-171 or the described sequences having at least 80% sequenceidentity to any one of SEQ ID NOs:1-171, and the working examples anddata set forth in Examples 1-11 of U.S. Patent Application PublicationNo. 2010-0199378 (U.S. patent application Ser. No. 12/515,687) areincorporated by reference herein.

In some cases, this document provides methods and materials involved intolerance of plants to low light conditions. For example, this documentprovides transgenic plants and seeds comprising nucleic acids encodingpolypeptides that confer tolerance to conditions of low light irradianceas described in U.S. Patent Application Publication No. 2010-0119688(U.S. patent application Ser. No. 12/307,561), which is incorporated byreference herein in its entirety. In some cases, a plant can include apolypeptide or nucleic acid or can be made to include a polypeptide ornucleic acid such that the sequence of such a polypeptide or nucleicacid is as set forth in one of the identified sequences of U.S. PatentApplication Publication No. 2010-0119688 (U.S. patent application Ser.No. 12/307,561) (e.g., SEQ ID NOs:1-146 of U.S. Patent ApplicationPublication No. 2010-0119688 (U.S. patent application Ser. No.12/307,561)), or is a homolog or ortholog thereof as described in U.S.Patent Application Publication No. 2010-0119688 (U.S. patent applicationSer. No. 12/307,561), or has at least 80% sequence identity (e.g., atleast 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity) to anidentified sequence of U.S. Patent Application Publication No.2010-0119688 (U.S. patent application Ser. No. 12/307,561), as set forthin U.S. Patent Application Publication No. 2010-0119688 (U.S. patentapplication Ser. No. 12/307,561). SEQ ID NOs:1-146 of U.S. PatentApplication Publication No. 2010-0119688 (U.S. patent application Ser.No. 12/307,561), together with the identified activities for each of SEQID NOs:1-146, the described homologs and orthologs of SEQ ID NOs:1-146and their associated activities, the sequences having at least 80%sequence identity (e.g., at least 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity) to SEQ ID NOs:1-146 and their associated activities,the phenotypes of plants containing any one of SEQ ID NOs:1-146 or thedescribed homologs of SEQ ID NOs:1-146 or the described orthologs of SEQID NOs:1-146 or the described sequences having at least 80% sequenceidentity to any one of SEQ ID NOs:1-146, and the working examples anddata set forth in Examples 1-22 of U.S. Patent Application PublicationNo. 2010-0119688 (U.S. patent application Ser. No. 12/307,561) areincorporated by reference herein.

In some cases, this document provides methods and materials involved inmodulating biomass levels in plants. For example, this document providesplants having increased biomass levels as well as materials and methodsfor making plants and plant products having increased biomass levels asdescribed in International Patent Application Publication No. WO2010/033564 and U.S. patent application Ser. No. 13/119,572, which areincorporated by reference herein in their entireties. In some cases, aplant can include a polypeptide or nucleic acid or can be made toinclude a polypeptide or nucleic acid such that the sequence of such apolypeptide or nucleic acid is as set forth in one of the identifiedsequences of International Patent Application Publication No. WO2010/033564 and U.S. patent application Ser. No. 13/119,572 (e.g., SEQID NOs:1-638 of International Patent Application Publication No. WO2010/033564 and U.S. patent application Ser. No. 13/119,572), or is ahomolog or ortholog thereof as described in International PatentApplication Publication No. WO 2010/033564 and U.S. patent applicationSer. No. 13/119,572, or has at least 80% sequence identity (e.g., atleast 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity) to anidentified sequence of International Patent Application Publication No.WO 2010/033564 and U.S. patent application Ser. No. 13/119,572, as setforth in International Patent Application Publication No. WO 2010/033564and U.S. patent application Ser. No. 13/119,572. SEQ ID NOs:1-638 ofInternational Patent Application Publication No. WO 2010/033564 and U.S.patent application Ser. No. 13/119,572, together with the identifiedactivities for each of SEQ ID NOs:1-638, the described homologs andorthologs of SEQ ID NOs:1-638 and their associated activities, thesequences having at least 80% sequence identity (e.g., at least 80%,85%, 90%, 95%, 97%, 98%, or 99% sequence identity) to SEQ ID NOs:1-638and their associated activities, the phenotypes of plants containing anyone of SEQ ID NOs:1-638 or the described homologs of SEQ ID NOs:1-638 orthe described orthologs of SEQ ID NOs:1-638 or the described sequenceshaving at least 80% sequence identity to any one of SEQ ID NOs:1-638,and the working examples and data set forth in Examples 1-11 ofInternational Patent Application Publication No. WO 2010/033564 and U.S.patent application Ser. No. 13/119,572 are incorporated by referenceherein.

The invention will be further described in the following examples, whichdo not limit the scope of the invention described in the claims.

VIII. EXAMPLES Example 1—Transgenic Arabidopsis Plants

The following symbols are used in the Examples with respect toArabidopsis transformation: T₁: first generation transformant; T₂:second generation, progeny of self-pollinated T₁ plants; T₃: thirdgeneration, progeny of self-pollinated T₂ plants; T₄: fourth generation,progeny of self-pollinated T₃ plants. Independent transformations arereferred to as events.

Nucleic acids were isolated from Arabidopsis thaliana plants, and clonedinto a Ti plasmid vector, CRS338 or CRS 811, under the control of a 35Spromoter. Each construct contained a phosphinothricin acetyltransferasegene which confers Finale™ resistance to transformed plants. Wild-typeArabidopsis thaliana ecotype Wassilewskija (Ws) plants were transformedseparately with each construct. The transformations were performedessentially as described in Bechtold et al., C.R. Acad. Sci. Paris,316:1194-1199 (1993).

Transgenic Arabidopsis lines containing SEQ ID NO:1, SEQ ID NO:69, SEQID NO:127, SEQ ID NO:315, SEQ ID NO:335, SEQ ID NO:454, SEQ ID NO:537,SEQ ID NO:568, SEQ ID NO:604, SEQ ID NO:632, SEQ ID NO:642, SEQ IDNO:848, SEQ ID NO:905, SEQ ID NO:951, SEQ ID NO:1023, SEQ ID NO:1045,SEQ ID NO: 1150, SEQ ID NO:1276, SEQ ID NO:1345, SEQ ID NO:1456, SEQ IDNO:1496. SEQ ID NO:1539, SEQ ID NO:1586, SEQ ID NO:1629, or SEQ IDNO:1634 were designated, ME05268, ME06120, ME09503, ME10007, ME10852,ME11939, ME12006, ME12596, ME12899, ME13456, ME15935, ME16594, ME16597,ME16630, ME17128, ME17578, ME18158. ME18314, ME18408, ME19304, ME19738,ME19971. ME20871, ME21199, or ME21508, respectively. The presence ofeach vector containing a nucleic acid described above in the respectivetransgenic Arabidopsis line transformed with the vector was confirmed byFinale™ resistance, PCR amplification from green leaf tissue extract,and/or sequencing of PCR products.

Example 2—Identification of Transgenic Plants Tolerant to Low LightConditions

Wild-type and transgenic seeds were sterilized, plated on solid 0.5×MSmedium containing 5 g/L sucrose, and stratified at 4° C. in the dark forthree days. After stratification, plates containing the seeds wereallowed to reach room temperature. The plates were then transferred to aConviron walk-in growth chamber (Controlled Environments Inc., Pambina,N. Dak.) at 22° C. and 70% humidity with a 16:8 hour light:dark cycle.Lighting was supplied by 32 watt fluorescent bulbs (Sylvania,F032/841/ECO, Danvers, Mass.), providing a red:far-red ratio of 13:1.The plates were covered with three layers of shade cloth (New York wire,charcoal fiberglass screen, 857650; Home Depot. Atlanta, Ga.) such thatthe irradiance was about 10 μmol/m²/s. The plates were rotated daily andmonitored for changes in hypocotyl elongation. After 48 hours, theplates were scored for late germinators, which were eliminated fromconsideration as candidate plants having reduced hypocotyl elongationunder low light conditions. Each seedling was transplanted to an 8×8 cmwell of a flat containing a total of 18 wells (three wells by six wells)and measuring 24 cm by 48 cm in size.

Seedlings maintained under conditions of irradiance with about 10μmol/m²/s of light for seven days at 22° C. were analyzed for hypocotyllength. The hypocotyls of individual seedlings were determined to be“long” or “short” based on qualitative observation (see, for example,FIG. 28).

Example 3-Identification of Transgenic Plants Tolerant to Short Day PlusEnd-of-Day-Far-Red(SD+EODFR) Conditions

A Short Day plus End-of-Day-Far-Red (SD+EODFR) assay was carried out onseedlings in order to evaluate the effect of SD+EODFR conditions onhypocotyl length. For the SD+EODFR assay, seeds were plated on 0.5%sucrose, 1×MS media (PhytoTech) agar plates, cold-treated for 3-4 daysat 4° C., then germinated for 2 days under continuous white light atabout 60 μmol/m²/s in walk-in Conviron growth chambers. Seedlings werethen exposed to SD+EODFR conditions for 4 days. SD+EODFR conditions were9.5 hours light, followed by a 30 minute pulse of far-red light at theend of each light cycle, alternating with 14 hours of darkness. TwoGro-Lux (Sylvania, 24660) and two Cool White (Phillips) lights at about60 μmol/m²/s PPFD, with a red:far-red ratio of about 5.5, were used forthe light cycle; the fluence rates under these conditions were:blue₄₅₀=12 μmol/m²/s, red₆₃₃=22 μmol/m²/s, far-red₇₄₀=4 μmol/m²/s,PPFD₄₀₀₋₇₀₀=55 μmol/m²/s. The far-red pulse was generated by 3 SNAP-LITEFar-red light boxes (Quantum devices, SL1515-670-735) at about 8μmol/m²/s PPFD, with a red:far-red ratio of about 0.14; the fluencerates under these conditions were: blue₄₅₀=0.004 μmol/m²/s, red₆₃₃=10μmol/m²/s, far-red₇₄₀=70 μmol/m²/s, PPFD₄₀₀₋₇₀₀=8 μmol/m²/s. Controlseedlings were cultured exactly as above except that they did notreceive the far-red pulse; that is, following germination, they wereexposed for two days to a cycle of 10 hours of light alternating with 14hours of darkness under 2 Gro-Lux and 2 Cool white lights at about 60μmol/m²/s PPFD, with a red:far-red ratio of about 5.5. Plates wererotated on the third day after plating and hypocotyl length wascharacterized on the fourth day after plating. The hypocotyls ofindividual seedlings were determined to be “long” or “short” based onqualitative observation (see, for example, FIG. 28).

Seedlings were then sprayed with sterile Finale® (concentration=0.63%),on two subsequent days, then allowed to grow for 24 hours beforechlorophyll fluorescence imaging was done to determine the Finale®resistant:Finale® sensitive ratio. Finale® sensitivity was determined byplacing plates of Finale® treated seedlings in a chlorophyllfluorescence imager (CF Imager, Technologica Limited, UK). Finale®resistant seedlings appeared red and Finale® sensitive seedlingsappeared blue. Hypocotyl lengths from Finale® resistant seedlings andFinale® sensitive seedlings were then subjected to a Chi-squaredanalysis to determine statistical significance.

Example 4—Results for ME05268, ME06120, ME09503, ME10007, ME10852,ME11939, ME13456, ME15935, ME16594, ME16597, ME16630, ME17128, ME17578,ME18158, ME18314, ME19304, ME19738, ME20871, ME21199, and ME21508 Events

T₃ and T₄ seed from event -03 of ME05268, T₂ and T₃ seed from event -04of ME05268. T₂ and T₃ seed from events -11 and -12 of ME06120, T₂ and T₃seed from events -03 and -07 of ME09503, T₂ and T₃ seed from events -02and -05 of ME10007, T₂ and T₃ seed from events -03 and -04 of ME10852,T₂ and T₃ seed from events -01, -02, and -03 of ME11939, T₂ and T₃ seedfrom events -02 and -05 of ME13456, T₂ and T₃ seed from events -03 and-04 of ME15935, T₃ and T₄ seed from events -02 and -05 of ME16594, T₂and T₃ seed from events -01, -04, and -06 of ME16597, T₂ and T₃ seedfrom events -01, -02, and -04 of ME16630, T₂ and T₃ seed from events-02, -03, and -03 of ME17128, T₂ and T₃ seed from events -01 and -03 ofME17578, T₂ and T₃ seed from events -01, -03, and -04 of ME18158, T₂ andT₃ seed from events -01, -02, 43, and -04 of ME18314, T₂ and T₃ seedfrom events -07 and -08 of ME19304, T₂ and T₃ seed from events -02 and-05 of ME19738, T₂ and T₃ seed from events -03, -05, and -10 of ME20871,T₂ and T₃ seed from events -01, -03 and -05 of ME21199, T₂ and T₃ seedfrom events -01 and -05 of ME21508 was grown under low light conditionsand evaluated for hypocotyl length as described in Example 2.

A Chi-square test was performed to compare transgenic seedlings andcorresponding non-transgenic segregants having a short or a longhypocotyl. A hypocotyl having a length similar to the hypocotyl lengthtypically exhibited by wild-type Arabidopsis seedlings grown undernormal light conditions (e.g., about 100 μmol/m²/s of white light) wasconsidered a short hypocotyl, whereas a hypocotyl having a lengthsimilar to that typically exhibited by wild-type Arabidopsis seedlingsgrown under low light conditions (e.g., about 10 μmol/m²/s of whitelight) was considered a long hypocotyl. Wild-type Arabidopsis seedsgrown for seven days at 22° C. under conditions of irradiance with about100 μmol/m²/s of white light and a 16:8 hour light:dark cycle typicallyform hypocotyls that are about 1-3 mm in length. Under conditions ofirradiance with about 10 μmol/m²/s of white light, the hypocotylstypically are about 5-7 mm in length.

Seedlings from event -03 of ME05268; event -04 of ME05268; events -11and -12 of ME06120; events 43 and -07 of ME09503; events -02 and -05 ofME10007; events -03 and -04 of ME10852; events -01, -02, and -03 ofME11939; events -02 and -05 of ME13456; events -03 and -04 of ME15935;events -02 and -05 of ME16594; events -01, -04, and 46 of ME16597;events -01, -02, and -04 of ME16630; events -02, -03, and -03 ofME17128; events -01 and -03 of ME17578; events -01, -03, and -04 ofME18158; events -01, -02, -03, and -04 of ME18314; events -07 and -08 ofME19304; events -02 and -05 of ME19738; events -03, -05, and -10 ofME20871; events -01, -03 and -05 of ME21199; and events -01 and -05 ofME21508 displayed a short hypocotyl under low light conditions in boththe T₂ and T₃ generations, and the transgene was linked to the shorthypocotyl phenotype with a confidence level of p<0.05 (Tables 1-23).

T₃ or T₄ data designated with -99 are data obtained from seed pooledfrom multiple individual plants of the indicated generation and event.

TABLE 1 Hypocotyl length in seedlings from ME05268 Short Long Hypo-Hypo- Chi- Plants cotyl cotyl Square p-value T₃ seedlings from event-03-99 32 6 54.35 1.68E−13 of ME05268 T₃ non-transgenic segregants of 037 event -03-99 of ME05268 T₄ seedlings from event -03- 69 3 53.001.68E−13 99-99 of ME05268 T₄ non-transgenic segregants of 0 7 event-03-99-99 of ME05268 T₂ seedlings from event -04 of 55 9 17.98 2.23E−05ME05268 T₂ non-transgenic segregants of 0 4 event -04 of ME05268 T₃seedlings from event -04-99 52 8 40.81 1.68E−10 of ME05268 T₃non-transgenic segregants of 0 14 event -04-99 of ME05268

TABLE 2 Hypocotyl length in seedlings from ME06120 Short Long Hypo-Hypo- Chi- Plants cotyl cotyl Square p-value T₂ seedlings from event -11of 26 4 16.89 3.96E−05 ME06120 T₂ non-transgenic segregants of 1 7 event-11 of ME05268 T₃ seedlings from event -11-99 52 3 37.89 7.48E−10 ofME06120 T₃ non-transgenic segregants of 4 13 event -11-99 of ME06120 T₂seedlings from event -12 of 27 2 14.43 1.45E−04 ME06120 T₂non-transgenic segregants of 0 2 event -12 of ME06120 T₃ seedlings fromevent -12-99 46 0 39.93 2.63E−10 of ME ME06120 T₃ non-transgenicsegregants of 1 4 event -12-99 of ME ME06120

TABLE 3 Hypocotyl length in seedlings from ME09503 Short Long Hypo-Hypo- Chi- Plants cotyl cotyl Square p-value T₂ seedlings from event -03of 34 4 35.47 2.59E−09 ME09503 T₂ non-transgenic segregants of 1 16event -03 of ME09503 T₃ seedlings from event -03-99 55 0 68.85 1.06E−16of ME09503 T₃ non-transgenic segregants of 1 18 event -03-99 of ME09503T₂ seedlings from event -07 of 46 1 44.94 2.03E−11 ME09503 T₂non-transgenic segregants of 2 12 event -07 of ME09503 T₃ seedlings fromevent -07-99 72 1 56.91 4.56E−14 of ME09503 T₃ non-transgenic segregantsof 1 6 event -07-99 of ME09503

TABLE 4 Hypocotyl length in seedlings from ME10007 Short Long Hypo-Hypo- Chi- Plants cotyl cotyl Square p-value T₂ seedlings from event -02of 57 3 42.15 8.45E−11 ME10007 T₂ non-transgenic segregants of 5 15event -02 of ME10007 T₃ seedlings from event -02-99 50 8 40.30 2.18E−10of ME10007 T₃ non-transgenic segregants of 2 19 event -02-99 of ME10007T₂ seedlings from event -05 of 58 0 37.14 1.10E−09 ME10007 T₂non-transgenic segregants of 9 11 event -05 of ME10007 T₃ seedlings fromevent -05-99 49 6 39.36 3.53E−10 of ME10007 T₃ non-transgenic segregantsof 3 18 event -05-99 of ME10007

TABLE 5 Hypocotyl length in seedlings from ME10852 Short Long Hypo-Hypo- Chi- Plants cotyl cotyl Square p-value T₂ seedlings from event -03of 57 1 48.97 2.59E−12 ME10852 T₂ non-transgenic segregants of 5 15event -03 of ME10852 T₃ seedlings from event -03-99 55 0 35.66 2.59E−09of ME10852 T₃ non-transgenic segregants of 11 13 event -03-99 of ME10852T₂ seedlings from event -04 of 57 0 71.00 3.57E−17 ME10852 T₂non-transgenic segregants of 0 14 event -04 of ME10852 T₃ seedlings fromevent -04-99 63 3 57.75 2.97E−14 of ME10852 T₃ non-transgenic segregantsof 0 11 event -04-99 of ME10852

TABLE 6 Hypocotyl length in seedlings from ME11939 Short Long Hypo-Hypo- Chi- Plants cotyl cotyl Square p-value T₂ seedlings from event -01of 32 6 29.39 5.93E−08 ME13 T₂ non-transgenic segregants of 0 13 event-01 of ME11939 T₃ seedlings from event -01-99 47 0 52.88 3.55E−13 ofME11939 T₃ non-transgenic segregants of 2 14 event -01-99 of ME11939 T₂seedlings from event -02 of 42 5 23.34 1.35E−06 ME11939 T₂non-transgenic segregants of 4 11 event -02 of ME11939 T₃ seedlings fromevent -02-99 46 2 44.94 2.03E−11 of ME11939 T₃ non-transgenic segregantsof 1 12 event -02-99 of ME11939 T₂ seedlings from event -05 of 45 827.72 1.40E−07 ME11939 T₂ non-transgenic segregants of 4 16 event -05 ofME11939 T₃ seedlings from event -05-99 33 0 27.59 1.50E−07 of ME11939 T₃non-transgenic segregants of 3 7 event -05-99 of ME11939

TABLE 7 Hypocotyl length in seedlings from ME13456 Short Long Hypo-Hypo- Chi- Plants cotyl cotyl Square p-value T₂ seedlings from event -02of 18 1 12.28 4.58E−04 ME13456 T₂ non-transgenic segregants of 3 6 event-02 of ME13456 T₃ seedlings from event -02-99 47 3 34.55 4.16E−09 ofME13456 T₃ non-transgenic segregants of 1 8 event -02-99 of ME13456 T₂seedlings from event -05 of 14 2 13.13 2.91E−04 ME13456 T₂non-transgenic segregants of 0 5 event -05 of ME13456 T₃ seedlings fromevent -05-99 21 3 23.42 1.30E−06 of ME13456 T₃ non-transgenic segregantsof 1 13 event -05-99 of ME13456

TABLE 8 Hypocotyl length in seedlings from ME15935 Short Long Hypo-Hypo- Chi- Plants cotyl cotyl Square p-value T₂ seedlings from event -03of 44 2 33.90 5.81E−09 ME15935 T₂ non-transgenic segregants of 2 12event -03 of ME15935 T₃ seedlings from event -03-99 53 3 51.86 5.97E−13of ME15935 T₃ non-transgenic segregants of 1 15 event -03-99 of ME15935T₂ seedlings from event -04 of 23 0 33.00 9.22E−09 ME15935 T₂non-transgenic segregants of 0 10 event -04 of ME15935 T₃ seedlings fromevent -04-99 58 0 41.24 1.34E−10 of ME15935 T₃ non-transgenic segregantsof 2 4 event -04-99 of ME15935

TABLE 9 Hypocotyl length in seedlings from ME16594 Short Long Hypo-Hypo- Chi- Plants cotyl cotyl Square p-value T₂ seedlings from event -02of 16 0 37.14 1.10E−09 ME16594 T₂ non-transgenic segregants of 12 52event -02 of ME16594 T₃ seedlings from event -02-99 46 10 10.18 1.42E−03of ME16594 T₃ non-transgenic segregants of 4 7 event -02-99 of ME16594T₂ seedlings from event -05 of 35 2 52.10 5.28E−13 ME16594 T₂non-transgenic segregants of 4 33 event -05 of ME16594 T₃ seedlings fromevent -05-99 41 11 5.14 2.34E−02 of ME16594 T₃ non-transgenic segregantsof 5 6 event -05-99 of ME16594

TABLE 10 Hypocotyl length in seedlings from ME16597 Short Long Hypo-Hypo- Chi- Plants cotyl cotyl Square p-value T₂ seedlings from event -01of 18 6 16.99 3.77E−05 ME16597 T₂ non-transgenic segregants of 0 11event -01 of ME16597 T₃ seedlings from event -01-99 69 3 55.76 8.20E−04of ME16597 T₃ non-transgenic segregants of 0 8 event -01-99 of ME16597T₂ seedlings from event -04 of 25 3 21.88 2.91E−06 ME16597 T₂non-transgenic segregants of 0 7 event -04 of ME16597 T₃ seedlings fromevent -04-99 54 5 32.49 1.20E−08 of ME16597 T₃ non-transgenic segregantsof 3 11 event -04-99 of ME16597 T₂ seedlings from event -04 of 44 534.14 5.12E−09 ME16597 T₂ non-transgenic segregants of 4 17 event -04 ofME16597 T₃ seedlings from event -04-99 49 4 43.99 3.30E−11 of ME16597 T₃non-transgenic segregants of 3 18 event -04-99 of ME16597

TABLE 11 Hypocotyl length in seedlings from ME16630 Short Long Hypo-Hypo- Chi- Plants cotyl cotyl Square p-value T₂ seedlings from event -01of 49 7 49.26 2.24E−12 ME16630 T₂ non-transgenic segregants of 0 20event -01 of ME16630 T₃ seedlings from event -01-99 59 1 55.63 8.75E−14of ME16630 T₃ non-transgenic segregants of 0 6 event -01-99 of ME16630T₂ seedlings from event -02 of 32 9 25.13 5.36E−07 ME16630 T₂non-transgenic segregants of 4 22 event -02 of ME16630 T₃ seedlings fromevent -02-99 43 6 33.59 6.79E−09 of ME16630 T₃ non-transgenic segregantsof 2 15 event -02-99 of ME16630 T₂ seedlings from event -04 of 60 919.53 9.89E−06 ME16630 T₂ non-transgenic segregants of 0 4 event -04 ofME16630 T₃ seedlings from event -04-99 65 9 12.14 4.94E−04 of ME16630 T₃non-transgenic segregants of 0 2 event -04-99 of ME16630

TABLE 12 Hypocotyl length in seedlings from ME17128 Short Long Hypo-Hypo- Chi- Plants cotyl cotyl Square p-value T₂ seedlings from event -02of 31 0 38.00 7.07E−10 ME17128 T₂ non-transgenic segregants of 0 7 event-02 of ME17128 T₃ seedlings from event -02-99 68 0 70.78 4.00E−17 ofME17128 T₃ non-transgenic segregants of 1 10 event -02-99 of ME17128 T₂seedlings from event -03 of 21 11 11.05 8.86E−04 ME17128 T₂non-transgenic segregants of 0 8 event -03 of ME17128 T₃ seedlings fromevent -03-99 74 0 80.00 3.74E−19 of ME17128 T₃ non-transgenic segregantsof 0 6 event -03-99 of ME17128 T₂ seedlings from event -04 of 28 4 18.062.14E−05 ME17128 T₂ non-transgenic segregants of 1 7 event -04 ofME17128 T₃ seedlings from event -04-99 62 0 39.42 3.41E−10 of ME17128 T₃non-transgenic segregants of 7 9 event -04-99 of ME17128

TABLE 13 Hypocotyl length in seedlings from ME17578 Short Long Chi-Plants Hypocotyl Hypocotyl Square p-value T₂ seedlings from event -01 of32 1 32.42 1.24E−08 ME17578 T₂ non-transgenic segregants of event - 0 601 of ME17578 T₃ seedlings from event -01-99 of 63 0 69.06 9.56E−17ME17578 T₃ non-transgenic segregants of event - 1 12 01-99 of ME17578 T₂seedlings from event -03 of 20 0 30.00 4.32E−08 ME17578 T₂non-transgenic segregants of event - 0 10 03 of ME17578 T₃ seedlingsfrom event -03-99 of 29 4 19.26 1.14E−05 ME17578 T₃ non-transgenicsegregants of event - 14 24 03-99 of ME17578

TABLE 14 Hypocotyl length in seedlings from ME18158 Short Long Chi-Plants Hypocotyl Hypocotyl Square p-value T₂ seedlings from event -01 of23 2 22.31 2.33E−06 ME18158 T₂ non-transgenic segregants of event - 2 1101 of ME18158 T₃ seedlings from event -01-99 of 61 0 54.93 1.25E−13ME18158 T₃ non-transgenic segregants of event - 1 5 01-99 of ME18158 T₂seedlings from event -02 of 25 5 7.62 5.78E−03 ME18158 T₂ non-transgenicsegregants of event - 0 2 02 of ME18158 T₃ seedlings from event -02-99of 70 0 7.88 5.01E−03 ME18158 T₃ non-transgenic segregants of event - 81 02-99 of ME18158 T₂ seedlings from event -04 of 22 3 27.17 1.86E−07ME18158 T₂ non-transgenic segregants of event - 0 13 04 of ME18158 T₃seedlings from event -04-99 of 22 3 49.13 2.40E−12 ME18158 T₃non-transgenic segregants of event - 0 13 04-99 of ME18158

TABLE 15 Hypocotyl length in seedlings from ME18314 Short Long Chi-Plants Hypocotyl Hypocotyl Square p-value T₂ seedlings from event -01 of13 14 5.72 1.67E−02 ME18314 T₂ non-transgenic segregants of event - 1 1101 of ME18314 T₃ seedlings from event -01-99 of 62 0 47.75 4.85E−12ME18314 T₃ non-transgenic segregants of event - 2 5 01-99 of ME18314 T₂seedlings from event -02 of 16 9 4.48 3.43E−02 ME18314 T₂ non-transgenicsegregants of event - 0 3 02 of ME18314 T₃ seedlings from event -02-99of 56 0 46.67 8.41E−12 ME18314 T₃ non-transgenic segregants of event - 410 02-99 of ME18314 T₂ seedlings from event -03 of 18 6 4.78 2.88E−02ME18314 T₂ non-transgenic segregants of event - 6 9 03 of ME18314 T₃seedlings from event -03-99 of 37 0 42.00 9.13E−11 ME18314 T₃non-transgenic segregants of event - 0 5 03-99 of ME18314 T₂ seedlingsfrom event -04 of 24 3 20.84 4.99E−06 ME18314 T₂ non-transgenicsegregants of event - 2 11 04 of ME18314 T₃ seedlings from event -04-99of 67 0 79.00 6.21E−19 ME18314 T₃ non-transgenic segregants of event - 012 04-99 of ME18314

TABLE 16 Hypocotyl length in seedlings from ME19304 Short Long Chi-Plants Hypocotyl Hypocotyl Square p-value T₂ seedlings from event -07 of28 1 29.22 6.48E−08 ME19304 T₂ non-transgenic segregants of event - 1 907 of ME19304 T₃ seedlings from event -07-99 of 57 0 40.51 1.95E−10ME19304 T₃ non-transgenic segregants of event - 8 12 07-99 of ME19304 T₂seedlings from event -08 of 18 11 7.67 5.62E−03 ME19304 T₂non-transgenic segregants of event - 0 6 08 of ME19304 T₃ seedlings fromevent -08-99 of 69 0 63.61 1.52E−15 ME19304 T₃ non-transgenic segregantsof event - 2 9 08-99 of ME19304

TABLE 17 Hypocotyl length in seedlings from ME19738 Short Long Chi-Plants Hypocotyl Hypocotyl Square p-value T₂ seedlings from event -02 of32 0 20.84 4.99E−06 ME19738 T₂ non-transgenic segregants of event - 0 702 of ME19738 T₃ seedlings from event -02-99 of 68 0 80.00 3.74E−19ME19738 T₃ non-transgenic segregants of event - 0 12 02-99 of ME19738 T₂seedlings from event -05 of 22 6 15.76 7.20E−05 ME19738 T₂non-transgenic segregants of event - 1 10 05 of ME19738 T₃ seedlingsfrom event -05-99 of 65 1 66.48 3.54E−16 ME19738 T₃ non-transgenicsegregants of event - 0 9 05-99 of ME19738

TABLE 18 Hypocotyl length in seedlings from ME20871 Short Long Chi-Plants Hypocotyl Hypocotyl Square p-value T₂ seedlings from event -03 of27 8 10.03 1.54E−03 ME20871 T₂ non-transgenic segregants of event - 0 403 of ME20871 T₃ seedlings from event -03-99 of 51 10 12.35 4.41E−04ME20871 T₃ non-transgenic segregants of event - 0 3 03-99 of ME20871 T₂seedlings from event -05 of 32 0 40.00 2.54E−10 ME20871 T₂non-transgenic segregants of event - 0 8 05 of ME20871 T₃ seedlings fromevent -05-99 of 61 0 68.52 1.26E−16 ME20871 T₃ non-transgenic segregantsof event - 1 13 05-99 of ME20871 T₂ seedlings from event -10 of 26 027.24 1.80E−07 ME20871 T₂ non-transgenic segregants of event - 1 6 10 ofME20871 T₃ seedlings from event -10-99 of 52 1 48.91 2.68E−12 ME20871 T₃non-transgenic segregants of event - 1 9 10-99 of ME20871

TABLE 19 Hypocotyl length in seedlings from ME21199 Short Long Chi-Plants Hypocotyl Hypocotyl Square p-value T₂ seedlings from event -01 of29 0 29.83 4.72E−08 ME21199 T₂ non-transgenic segregants of event - 1 601 of ME21199 T₃ seedlings from event -01-99 of 62 0 78.00 1.03E−18ME21199 T₃ non-transgenic segregants of event - 0 16 01-99 of ME21199 T₂seedlings from event -03 of 19 0 9.44 2.12E−03 ME21199 T₂ non-transgenicsegregants of event - 7 5 03 of ME21199 T₃ seedlings from event -03-99of 68 0 55.03 1.19E−13 ME21199 T₃ non-transgenic segregants of event - 38 03-99 of ME21199 T₂ seedlings from event -05 of 26 0 20.41 6.26E−06ME21199 T₂ non-transgenic segregants of event - 4 7 05 of ME21199 T₃seedlings from event -05-99 of 31 1 17.88 2.35E−05 ME21199 T₃non-transgenic segregants of event - 5 7 05-99 of ME21199

TABLE 20 Hypocotyl length in seedlings from ME21508 Short Long Chi-Plants Hypocotyl Hypocotyl Square p-value T₂ seedlings from event -01 of20 5 15.76 7.19E−05 ME21508 T₂ non-transgenic segregants of event - 2 1201 of ME21508 T₃ seedlings from event -01-99 of 74 0 80.00 3.74E−19ME21508 T₃ non-transgenic segregants of event - 0 6 01-99 of ME21508 T₂seedlings from event -05 of 23 8 15.71 7.85E−05 ME21508 T₂non-transgenic segregants of event - 0 9 05 of ME21508 T₃ seedlings fromevent -05-99 of 65 0 78.00 1.03E−18 ME21508 T₃ non-transgenic segregantsof event - 0 13 05-99 of ME21508

There were no observable or statistically significant differencesbetween T₂ ME05268, ME06120, ME09503, ME10007, ME10852, ME11939,ME13456, ME15935, ME16594, ME16597, ME16630, ME17128, ME17578, ME18158,ME18314, ME19304, ME19738. ME20871, ME21199, and ME21508 plants andcontrol plants in germination, onset of flowering, rosette area,fertility, and general morphology/architecture.

Example 5—Results for ME12006, ME12596, and ME12899 Events

T₂ and T₃ seed from events -03, -02, and -03 of ME12006, T₂ and T₃ seedfrom events -08 and -09 of ME12596, and T₂ and T₃ seed from events -05and -06 of ME12899 was grown under SD+EODFR conditions and evaluated forhypocotyl length as described in Example 3.

Seedlings from events -03, -02, and -03 of ME12006; events -08 and -09of ME12596; and events -05 and -06 of ME12899 displayed a shorthypocotyl under SD+EODFR conditions in both the T₂ and T₃ generations,and the transgene was linked to the short hypocotyl phenotype with aconfidence level of p<0.05 (Tables 21-23).

TABLE 21 Hypocotyl length in seedlings from ME12006 Short Long Chi-Plants Hypocotyl Hypocotyl Square p-value T₂ seedlings from event -01 of22 2 8.89 2.87E−03 ME12006 T₂ non-transgenic segregants of event - 8 801 of ME12006 T₃ seedlings from event -01-03 of 27 3 7.50 6.17E−03ME12006 T₃ non-transgenic segregants of event - 5 5 01-03 of ME12006 T₂seedlings from event -02 of 20 20 12.23 4.70E−04 ME12006 T₂non-transgenic segregants of event - 6 10 02 of ME12006 T₃ seedlingsfrom event -02-01 of 23 4 12.61 3.84E−04 ME12006 T₃ non-transgenicsegregants of event - 2 7 02-01 of ME12006 T₂ seedlings from event -03of 24 4 7.94 4.83E−03 ME12006 T₂ non-transgenic segregants of event - 46 03 of ME12006 T₃ seedlings from event -03-04 of 19 2 8.82 2.99E−03ME12006 T₃ non-transgenic segregants of event - 2 4 03-04 of ME12006

TABLE 22 Hypocotyl length in seedlings from ME12596 Short Long Chi-Plants Hypocotyl Hypocotyl Square p-value T₂ seedlings from event -08 ofME12596 22 4 18.75 1.487E−05  T₂ non-transgenic segregants of 2 12 event-08 of ME12596 T₃ seedlings from event -08-01 of 18 4 10.21 1.40E−04ME12596 T₃ non-transgenic segregants of 4 10 event -08-01 of ME12596 T₂seedlings from event -09 of 21 5 8.12 4.39E−03 ME12596 T₂ non-transgenicsegregants of 5 9 event -09 of ME12596 T₃ seedlings from event -09-01 of20 4 5.08 2.42E−02 ME12596 T₃ non-transgenic segregants of 8 8 event-09-01 of ME12596

TABLE 23 Hypocotyl length in seedlings from ME12899 Short Long Chi-Plants Hypocotyl Hypocotyl Square p-value T₂ seedlings from event -05 ofME12899 24 4 10.98 9.23E−04 T₂ non-transgenic segregants of 4 8 event-05 of ME12899 T₃ seedlings from event -05-99 of 27 3 7.5 6.17E−03ME12899 T₃ non-transgenic segregants of 5 5 event -05-99 of ME12899 T₂seedlings from event -06 of 26 2 23.22 1.445E−06 ME12899 T₂non-transgenic segregants of 2 10 event -06 of ME12899 T₃ seedlings fromevent -06-99 of 21 3 6.77 9.264E−03 ME12899 T₃ non-transgenic segregantsof 8 8 event -06-99 of ME12899

There were no observable or statistically significant differencesbetween T₂ ME12006, ME12596, and ME12899 plants and control plants ingermination, onset of flowering, rosette area, fertility, and generalmorphology/architecture.

Example 6—Results for ME18408 and ME19971 Events

T₂ and T₃ seed from events -01, -02, and -03 of ME18408, and T₂ and T₃seed from events -01, -02, -03, and -05 of ME19971 was grown under lowlight conditions and SD+EODFR conditions as described in Examples 2 and3, respectively, and evaluated for hypocotyl length.

Seedlings from events -01, -02, and -03 of ME18408, and events -01, -02,-03, and -05 of ME19971 displayed a short hypocotyl under SD+EODFRconditions in both the T₂ and T₃ generations, and the transgene waslinked to the short hypocotyl phenotype with a confidence level ofp<0.05 (Tables 24 and 26). Seedlings from events -01, and -02 ofME18408, and events -01, -02, -03, and -05 of ME19971 displayed a shorthypocotyl under SD+EODFR conditions in both the T₂ and T₃ generations,and the transgene was linked to the short hypocotyl phenotype with aconfidence level of p<0.05 (Tables 25 and 27).

TABLE 24 Hypocotyl length in seedlings from ME18408 grown under lowlight conditions Short Long Chi- Plants Hypocotyl Hypocotyl Squarep-value T₂ seedlings from event -01 of 63 2 44.58 2.44E−11 ME18408 T₂non-transgenic segregants of event - 0 4 01 of ME18408 T₃ seedlings fromevent -01-99 of 40 6 35.90 2.08E−09 ME18408 T₃ non-transgenic segregantsof event - 1 16 01-99 of ME18408 T₂ seedlings from event -02 of 38 728.67 8.58E−08 ME18408 T₂ non-transgenic segregants of event - 3 17 02of ME18408 T₃ seedlings from event -02-99 of 39 17 10.98 9.20E−04ME18408 T₃ non-transgenic segregants of event - 5 14 02-99 of ME18408 T₂seedlings from event -03 of 30 1 25.76 3.86E−07 ME18408 T₂non-transgenic segregants of event - 7 15 03 of ME18408 T₃ seedlingsfrom event -03-99 of 23 5 21.74 3.12E−06 ME18408 T₃ non-transgenicsegregants of event - 11 32 03-99 of ME18408

TABLE 25 Hypocotyl length in seedlings from ME18408 grown under SD +EODFR conditions Short Long Chi- Plants Hypocotyl Hypocotyl Squarep-value T₂ seedlings from event -01 of 22 5 6.18 1.29E−02 ME18408 T₂non-transgenic segregants of event - 5 7 01 of ME18408 T₃ seedlings fromevent -01-99 of 19 8 10.71 1.06E−03 ME18408 T₃ non-transgenic segregantsof event - 1 9 01-99 of ME18408 T₂ seedlings from event -02 of 25 5 4.443.50E−02 ME18408 T₂ non-transgenic segregants of event - 5 5 02 ofME18408 T₃ seedlings from event -02-99 of 22 3 6.8 9.13E−03 ME18408 T₃non-transgenic segregants of event - 7 7 02-99 of ME18408

TABLE 26 Hypocotyl length in seedlings from ME19971 grown under lowlight conditions Short Long Chi- Plants Hypocotyl Hypocotyl Squarep-value T₂ seedlings from event -01 of 8 0 18.00 2.21E−05 ME19971 T₂non-transgenic segregants of event - 0 10 01 of ME19971 T₃ seedlingsfrom event -01-99 of 37 0 61.00 5.71E−15 ME19971 T₃ non-transgenicsegregants of event - 0 24 01-99 of ME19971 T₂ seedlings from event -02of 16 2 19.64 9.37E−06 ME19971 T₂ non-transgenic segregants of event - 09 02 of ME19971 T₃ seedlings from event -02-99 of 36 0 29.19 6.56E−08ME19971 T₃ non-transgenic segregants of event - 1 3 02-99 of ME19971 T₂seedlings from event -03 of 14 1 19.08 1.25E−05 ME19971 T₂non-transgenic segregants of event - 0 8 03 of ME19971 T₃ seedlings fromevent -03-99 of 34 0 46.00 1.18E−11 ME19971 T₃ non-transgenic segregantsof event - 0 12 03-99 of ME19971 T₂ seedlings from event -05 of 26 029.00 7.24E−08 ME19971 T₂ non-transgenic segregants of event - 0 3 05 ofME19971 T₃ seedlings from event -05-99 of 42 0 47.94 4.39E−12 ME19971 T₃non-transgenic segregants of event - 3 16 05-99 of ME19971

TABLE 27 Hypocotyl length in seedlings from ME19971 grown under SD +EODFR conditions Short Long Chi- Plants Hypocotyl Hypocotyl Squarep-value T₂ seedlings from event -01 of ME19971 30 2 30.00 4.32E−08 T₂non-transgenic segregants of 0 8 event -01 of ME19971 T₃ seedlings fromevent -01-04 of 22 0 32.00 1.542E−08 ME19971 T₃ non-transgenicsegregants of 0 10 event -01-04 of ME19971 T₂ seedlings from event -02of 24 4 17.60 2.721E−05 ME19971 T₂ non-transgenic segregants of 2 10event -02 of ME19971 T₃ seedlings from event -02-04 of 22 6 16.165.811E−05 ME19971 T₃ non-transgenic segregants of 0 8 event -02-04 ofME19971 T₂ seedlings from event -03 of 28 0 40.00 2.54E−10 ME19971 T₂non-transgenic segregants of 0 12 event -03 of ME19971 T₃ seedlings fromevent -03-06 of 24 0 17.49 2.895E−05 ME19971 T₃ non-transgenicsegregants of 4 6 event -03-06 of ME19971 T₂ seedlings from event -05 of24 2 24.35 8.034E−07 ME19971 T₂ non-transgenic segregants of 2 12 event-05 of ME19971 T₃ seedlings from event -05-02 of 25 4 6.13 1.33E−02ME19971 T₃ non-transgenic segregants of 3 4 event -05-02 of ME19971

There were no observable or statistically significant differencesbetween T₂ ME18408 and ME19971 plants and control plants in germination,onset of flowering, rosette area, fertility, and generalmorphology/architecture.

Example 7—Determination of Functional Homologs by Reciprocal BLAST

A candidate sequence was considered a functional homolog of a referencesequence if the candidate and reference sequences encoded proteinshaving a similar function and/or activity. A process known as ReciprocalBLAST (Rivera el al., Proc. Natl. Acad. Sci. USA, 95:6239-6244 (1998))was used to identify potential functional homolog sequences fromdatabases consisting of all available public and proprietary peptidesequences, including NR from NCBI and peptide translations from Ceresclones.

Before starting a Reciprocal BLAST process, a specific referencepolypeptide was searched against all peptides from its source speciesusing BLAST in order to identify polypeptides having BLAST sequenceidentity of 80% or greater to the reference polypeptide and an alignmentlength of 85% or greater along the shorter sequence in the alignment.The reference polypeptide and any of the aforementioned identifiedpolypeptides were designated as a cluster.

The BLASTP version 2.0 program from Washington University at SaintLouis. Mo., USA was used to determine BLAST sequence identity andE-value. The BLASTP version 2.0 program includes the followingparameters: 1) an E-value cutoff of 1.0e-5; 2) a word size of 5; and 3)the -postsw option. The BLAST sequence identity was calculated based onthe alignment of the first BLAST HSP (High-scoring Segment Pairs) of theidentified potential functional homolog sequence with a specificreference polypeptide. The number of identically matched residues in theBLAST HSP alignment was divided by the HSP length, and then multipliedby 100 to get the BLAST sequence identity. The HSP length typicallyincluded gaps in the alignment, but in some cases gaps were excluded.

The main Reciprocal BLAST process consists of two rounds of BLASTsearches; forward search and reverse search. In the forward search step,a reference polypeptide sequence, “polypeptide A,” from source speciesSA was BLASTed against all protein sequences from a species of interest.Top hits were determined using an E-value cutoff of 10⁻⁵ and a sequenceidentity cutoff of 35%. Among the top hits, the sequence having thelowest E-value was designated as the best hit, and considered apotential functional homolog or ortholog. Any other top hit that had asequence identity of 80% or greater to the best hit or to the originalreference polypeptide was considered a potential functional homolog orortholog as well. This process was repeated for all species of interest.

In the reverse search round, the top hits identified in the forwardsearch from all species were BLASTed against all protein sequences fromthe source species SA. A top hit from the forward search that returned apolypeptide from the aforementioned cluster as its best hit was alsoconsidered as a potential functional homolog.

Functional homologs were identified by manual inspection of potentialfunctional homolog sequences. Representative functional homologs for SEQID NO:3, SEQ ID NO:70, SEQ ID NO:129, SEQ ID NO:317, SEQ ID NO:337, SEQID NO:456, SEQ ID NO:538, SEQ ID NO:570, SEQ ID NO:606, SEQ ID NO:634,SEQ ID NO:644, SEQ ID NO:850, SEQ ID NO:907, SEQ ID NO:953, SEQ IDNO:1024, SEQ ID NO:1047, SEQ ID NO:1151, SEQ ID NO:1277, SEQ ID NO:1347,SEQ ID NO:1457, SEQ ID NO:1497, SEQ ID NO:1540, SEQ ID NO:1587, SEQ IDNO:1630, and SEQ ID NO:1635 are shown in FIGS. 1-24, respectively.

Example 8—Determination of Functional Homologs Bi Hidden Markov Models

Hidden Markov Models (HMMs) were generated by the program HMMER 2.3.2.To generate each HMM, the default HMMER 2.3.2 program parameters,configured for glocal alignments, were used.

An HMM was generated using the sequences shown in FIG. 1 as input. Thesesequences were fitted to the model and a representative HMM bit scorefor each sequence is shown in the Sequence Listing. Additional sequenceswere fitted to the model, and representative HMM bit scores for any suchadditional sequences are shown in the Sequence Listing. The resultsindicate that these additional sequences are functional homologs of SEQID NO:3.

The procedure above was repeated and an HMM was generated for each groupof sequences shown in FIGS. 2-24, using the sequences shown in eachFigure as input for that HMM. A representative bit score for eachsequence is shown in the Sequence Listing. Additional sequences werefitted to certain HMMs, and representative HMM bit scores for suchadditional sequences are shown in the Sequence Listing. The resultsindicate that these additional sequences are functional homologs of thesequences used to generate that HMM.

Example 9—Identification of Transgenic Plants Exhibiting a RedLight-Specific Short Hypocotyl Phenotype

Wild type and transgenic seeds were surface-sterilized, plated on solid0.5×MS medium containing 5 g/L sucrose, 0.5 g/L MES, 7 g/L Agar(adjusted to pH 5.7), and stratified at 4° C. in the dark for three tofour days. After stratification, plates were acclimated to roomtemperature, wrapped in micropore tape, and exposed to continuous whitelight having a fluence rate of ˜60 μmol/m²/s PAR, and a red:far-redratio (R:FR) of -5.3. After 24 hours, plates from wild type controls andtransgenic lines were moved to one of three light conditions: (1) whitelight conditions at a lower fluence rate (˜15 μmol/m²/s PAR, R:FR=˜5.0),(2) red-light conditions (SNAP-LITE™ Red/Far-Red light box (QuantumDevices), at -15 μmol/m²/s PAR, R:FR=˜80), or (3) far-red conditions(SNAP-LITE™ Red/Far-red light box, at -15 μmol/m²/s PAR, R:FR=˜0.10).Seedlings were maintained under continuous light conditions for fivedays. The hypocotyls of individual seedlings were determined to be“tall” or “short” based on qualitative observation.

A hypocotyl having a length similar to the hypocotyl length typicallyexhibited by wild-type Arabidopsis seedlings grown under the same lightconditions was considered a tall hypocotyl. A hypocotyl having reducedlength relative to the hypocotyl length typically exhibited by wild-typeArabidopsis seedlings grown under the same light conditions wasconsidered a short hypocotyl. Transgenic seedlings from ten CeresSEEDLINE ID nos, failed to germinate, or germinated poorly, undercontinuous red light (ME10007, ME10852, ME11961, ME15935, ME17128,ME18158, ME18314, ME19304, ME20871, and ME21508).

Transgenic seedlings from eight Ceres SEEDLINE ID nos. (ME11939,ME16630, ME19971, ME05268, ME13456, ME13629, ME16597, and ME17578)exhibited short hypocotyls when grown under continuous red light.Transgenic seedlings from three of these (ME11939, ME16630, and ME19971)exhibited tall hypocotyls under continuous far-red light exposure,indicating that the short hypocotyl phenotype was red-light specific inthese three seed lines. In contrast, the other five seedlings (ME05268,ME13456, ME13629, ME16597, and ME17578) exhibited a short-hypocotylphenotype when grown under far-red light, indicating that theshort-hypocotyl phenotype exhibited by ME05268, ME13456, ME13629,ME16597, and ME17578 was not red-light specific (See, e.g., Parks andSpaulding, Proc. Natl. Acad. Sci., 96: 14142-14146 (1999) describingdifferent molecular mechanisms for suppression of hypocotyl elongationunder continuous red and far-red light conditions).

A similar red light-dependent short hypocotyl phenotype has beenobserved in transgenic plants overexpressing the photochemically andbiologically functional photoreceptor, Phytochrome B (Phy B) (Wagner etal., Plant Cell, 3: 1275-1288 (1991)). Phy B null mutants exhibit a longhypocotyl seedling phenotype and increased plant height (Kebrom andBrutnell, J Exp. Bot., 58: 3079-3089 (2007)). These observations suggestthat transgene modulation of light response pathways can produce plantsexhibiting either increased grain yield, or increased biomass. SeePennell et al., U.S. Pat. App. Ser. No. 61/097,789, “Transgenic PlantsHaving Increased Biomass,” filed Sep. 17, 2008, incorporated byreference herein. Thus, transgenic plants comprising nucleic acidsequences that down-regulate expression of a At5g14370 polypeptide (SEQID NO: 456) (FIG. 6), a At1g13360 polypeptide (SEQ ID NO: 953) (FIG.11), a At2g35940 polypeptide (SEQ ID NO: 1540) (FIG. 21), and sequencesidentified as functional homologs of these sequences (see FIGS. 6, 11,21 and sequence listing) are predicted to exhibit a tall hypocotylphenotype under conditions of normal or low light.

OTHER EMBODIMENTS

It is to be understood that while the invention has been described inconjunction with the detailed description thereof, the foregoingdescription is intended to illustrate and not limit the scope of theinvention, which is defined by the scope of the appended claims. Otheraspects, advantages, and modifications are within the scope of thefollowing claims.

1. A method of modulating a trait in a plant, said method comprisingintroducing into a plant cell an exogenous nucleic acid, said exogenousnucleic acid comprising a regulatory region operably linked to: anucleotide sequence encoding a polypeptide having 90 percent or greatersequence identity to an amino acid sequence selected from the groupconsisting of SEQ ID NO:3 and SEQ ID NO:634; producing a plant from saidplant cell; and selecting a plant for increased low light tolerance orSD+EODFR tolerance as compared to a control plant that does not comprisesaid nucleic acid.
 2. A plant cell comprising an exogenous nucleic acid,said exogenous nucleic acid comprising a regulatory region operablylinked to: a nucleotide sequence encoding a polypeptide having 90percent or greater sequence identity to an amino acid sequence selectedfrom the group consisting of SEQ ID NO:3 and SEQ ID NO:634: wherein aplant produced from said cell has increased low light tolerance orSD+EODFR tolerance as compared to a control plant that does not comprisesaid nucleic acid.
 3. A plant comprising an exogenous nucleic acid, saidexogenous nucleic acid comprising: (a) a nucleotide sequence encoding apolypeptide having 90 percent or greater sequence identity to an aminoacid sequence selected from the group consisting of SEQ ID NO:3 and SEQID NO:634; wherein the plant has increased low light tolerance orSD+EODFR tolerance as compared to a control plant that does not comprisesaid nucleic acid.
 4. The method of claim 1, wherein said polypeptidehas 95 percent or greater sequence identity to an amino acid sequenceselected from the group consisting of SEQ ID NO:3 and SEQ ID NO:634. 5.The method of claim 1, wherein said polypeptide sequence comprises SEQID NO:3 or SEQ ID NO:634.
 6. The method of claim 1, wherein saidnucleotide sequence comprises SEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO:632,or SEQ ID NO:633.
 7. The plant of claim 3, wherein said polypeptide has95 percent or greater sequence identity to an amino acid sequenceselected from the group consisting of SEQ ID NO:3 and SEQ ID NO:634. 8.The plant of claim 3, wherein said polypeptide sequence comprises SEQ IDNO:3 or SEQ ID NO:634.
 9. The plant of claim 3, wherein said nucleotidesequence comprises SEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO:632, or SEQ IDNO:633.